1
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Sanchez Gonzalez MDC, Kamerling P, Iermito M, Casati S, Riaz U, Veal CD, Maini M, Jeanson F, Benhamed OM, van Enckevort E, Landi A, Mimouni Y, Le Cornec C, Coviello DA, Franchin T, Fusco F, Ramírez García JA, van der Zanden LFM, Bernier A, Wilkinson MD, Mueller H, Gibson SJ, Brookes AJ. Common conditions of use elements. Atomic concepts for consistent and effective information governance. Sci Data 2024; 11:465. [PMID: 38719810 PMCID: PMC11078919 DOI: 10.1038/s41597-024-03279-z] [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: 06/23/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse 'use conditions'. We report a core lexicon of terms that are atomic, non-directional 'concepts of use', called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.
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Affiliation(s)
| | - Pim Kamerling
- VASCERN ERN & Radboud University Medical Center - Center for Radiology and Nuclear Medicine, Geert Grooteplein Zuid 26-28 (route 260), 6525 GA, Nijmegen, The Netherlands
| | - Mariapia Iermito
- Istituto Neurologico "Carlo Besta" |, Fondazione IRCCS Via Giovanni Celoria, 11, 20133, Milano, MI, Italy
| | - Sara Casati
- BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Umar Riaz
- Dept. Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Colin D Veal
- Dept. Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Monika Maini
- Dept. Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Francis Jeanson
- Ontario Brain Institute, Centre for Analytics, 1 Richmond St. West, Suite 400, Toronto, Ontario, M5H3W4, Canada
| | - Oussama Mohammed Benhamed
- Departamento de Biotecnología-Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, Nederland
| | - Annalisa Landi
- Fondazione per la Ricerca Farmacologica Gianni Benzi onlus, Via Giulio Petroni, 91/D, 70124, Bari, Italy
| | - Yanis Mimouni
- Thematic Institute of Genetics, Genomics & Bioinformatics, INSERM, Paris, 75013, France
| | - Clèmence Le Cornec
- Pediatric Nephrology Division, Center for Pediatrics and Adolescent Medicine, Heidelberg University Hospita, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Domenico A Coviello
- Dept. Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy
| | - Tiziana Franchin
- Research Biobank, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Fusco
- Institute of Genetics and Biophysics "Adriano Buzzati- Traverso" IGB-ABT, Department of Biomedical Sciences (DSB), National Research Council (CNR), Via P. Castellino 111, 80131, Naples, Italy
| | - Jose Antonio Ramírez García
- Pediatric Nephrology Division, Center for Pediatrics and Adolescent Medicine, Heidelberg University Hospita, Im Neuenheimer Feld 130.3, 69120, Heidelberg, Germany
| | - Loes F M van der Zanden
- ERN for Rare Urogenital Diseases and Complex Conditions (ERN eUROGEN), department of Urology & IQ Health science department, Radboud university medical center, Geert Grooteplein Zuid 10, 6525 GA, Nijmegen, the Netherlands
| | - Alexander Bernier
- Centre of Genomics and Policy, McGill University, Faculty of Medicine and Health Sciences, 740, avenue Dr. Penfield, suite 5200, Montreal, Quebec, H3A 0G1, Canada
| | - Mark D Wilkinson
- Departamento de Biotecnología-Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Heimo Mueller
- BBMRI-ERIC, Neue Stiftingtalstrasse 2/B/6, 8010, Graz, Austria
| | - Spencer J Gibson
- Dept. Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Anthony J Brookes
- Dept. Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
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2
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Jeanson F, Gibson SJ, Alper P, Bernier A, Woolley JP, Mietchen D, Strug A, Becker R, Kamerling P, Sanchez Gonzalez MDC, Mah N, Novakowski A, Wilkinson MD, Benhamed OM, Landi A, Krog GP, Müller H, Riaz U, Veal C, Holub P, van Enckevort E, Brookes AJ. Getting your DUCs in a row - standardising the representation of Digital Use Conditions. Sci Data 2024; 11:464. [PMID: 38719839 PMCID: PMC11078994 DOI: 10.1038/s41597-024-03280-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Improving patient care and advancing scientific discovery requires responsible sharing of research data, healthcare records, biosamples, and biomedical resources that must also respect applicable use conditions. Defining a standard to structure and manage these use conditions is a complex and challenging task. This is exemplified by a near unlimited range of asset types, a high variability of applicable conditions, and differing applications at the individual or collective level. Furthermore, the specifics and granularity required are likely to vary depending on the ultimate contexts of use. All these factors confound alignment of institutional missions, funding objectives, regulatory and technical requirements to facilitate effective sharing. The presented work highlights the complexity and diversity of the problem, reviews the current state of the art, and emphasises the need for a flexible and adaptable approach. We propose Digital Use Conditions (DUC) as a framework that addresses these needs by leveraging existing standards, striking a balance between expressiveness versus ambiguity, and considering the breadth of applicable information with their context of use.
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Grants
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- 825575 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)
- Algerian Ministry of Higher Education and Scientific Research
- The European Reference Network on Rare Multisystemic Vascular Diseases (VASCERN), which is partly co-funded by the European Union within the framework of the EU4Health programme – “VASCERN Action Grant".
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Affiliation(s)
- Francis Jeanson
- Centre for Analytics, Ontario Brain Institute, Toronto, Canada.
| | - Spencer J Gibson
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Pinar Alper
- Luxembourg National Data Service, Esch-sur-Alzette, Luxembourg
| | - Alexander Bernier
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Canada
| | - J Patrick Woolley
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Andrzej Strug
- Medical Laboratory Diagnostics Department, Medical University of Gdańsk, Gdańsk, Poland
| | - Regina Becker
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pim Kamerling
- Center for Radiology and Nuclear Medicine, VASCERN ERN /Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Nancy Mah
- Biomedical Data & Bioethics Group, Fraunhofer Institute for Biomedical Engineering, Sulzbach/Saar, Germany
| | | | - Mark D Wilkinson
- Departamento de Biotecnología-Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, Spain
| | - Oussama Mohammed Benhamed
- Departamento de Biotecnología-Biología Vegetal, ETSI Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, Spain
| | - Annalisa Landi
- Research, Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, Bari, Italy
| | | | | | - Umar Riaz
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Colin Veal
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Institute of Computer Science, Masaryk University, Brno, Czechia
| | - Esther van Enckevort
- University of Groningen, Groningen, Netherlands
- Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
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3
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Eklund N, Engels C, Neumann M, Strug A, van Enckevort E, Baber R, Bloemers M, Debucquoy A, van der Lugt A, Müller H, Parkkonen L, Quinlan PR, Urwin E, Holub P, Silander K, Anton G. Update of the Minimum Information About BIobank Data Sharing (MIABIS) Core Terminology to the 3 rd Version. Biopreserv Biobank 2024. [PMID: 38497765 DOI: 10.1089/bio.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Introduction: The Minimum Information About BIobank Data Sharing (MIABIS) is a biobank-specific terminology enabling the sharing of biobank-related data for different purposes across a wide range of database implementations. After 4 years in use and with the first version of the individual-level MIABIS component Sample, Sample donor, and Event, it was necessary to revise the terminology, especially to include biobanks that work more in the data domain than with samples. Materials & Methods: Nine use-cases representing different types of biobanks, studies, and networks participated in the development work. They represent types of data, specific sample types, or levels of organization that were not included earlier in MIABIS. To support our revision of the Biobank entity, we conducted a survey of European biobanks to chart the services they provide. An important stakeholder group for biobanks include researchers as the main users of biobanks. To be able to render MIABIS more researcher-friendly, we collected different sample/data requests to analyze the terminology adjustment needs in detail. During the update process, the Core terminology was iteratively reviewed by a large group of experts until a consensus was reached. Results: With this update, MIABIS was adjusted to encompass data-driven biobanks and to include data collections, while also describing the services and capabilities biobanks offer to their users, besides the retrospective samples. The terminology was also extended to accommodate sample and data collections of nonhuman origin. Additionally, a set of organizational attributes was compiled to describe networks. Discussion: The usability of MIABIS Core v3 was increased by extending it to cover more topics of the biobanking domain. Additionally, the focus was on a more general terminology and harmonization of attributes with the individual-level entities Sample, Sample donor, and Event to keep the overall terminology minimal. With this work, the internal semantics of the MIABIS terminology was improved.
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Affiliation(s)
- Niina Eklund
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Cäcilia Engels
- German Biobank Node (GBN), Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Charité University Hospital Berlin, Berlin, Germany
| | | | - Andrzej Strug
- Department of Medical Laboratory Diagnostics, Medical University of Gdansk, Gdansk, Poland
| | - Esther van Enckevort
- University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ronny Baber
- Leipzig Medical Biobank, Leipzig, Germany and Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig Medical Center, Leipzig, Germany
| | - Margreet Bloemers
- ZonMw Organisation for Health Research and Development, the Hague, The Netherlands
| | | | | | | | - Lauri Parkkonen
- Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland
| | | | - Esmond Urwin
- University of Nottingham, Nottingham, United Kingdom
| | | | - Kaisa Silander
- Finnish Institute for Health and Welfare, Helsinki, Finland
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4
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Akyüz K, Cano Abadía M, Goisauf M, Mayrhofer MT. Unlocking the potential of big data and AI in medicine: insights from biobanking. Front Med (Lausanne) 2024; 11:1336588. [PMID: 38357641 PMCID: PMC10864616 DOI: 10.3389/fmed.2024.1336588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Big data and artificial intelligence are key elements in the medical field as they are expected to improve accuracy and efficiency in diagnosis and treatment, particularly in identifying biomedically relevant patterns, facilitating progress towards individually tailored preventative and therapeutic interventions. These applications belong to current research practice that is data-intensive. While the combination of imaging, pathological, genomic, and clinical data is needed to train algorithms to realize the full potential of these technologies, biobanks often serve as crucial infrastructures for data-sharing and data flows. In this paper, we argue that the 'data turn' in the life sciences has increasingly re-structured major infrastructures, which often were created for biological samples and associated data, as predominantly data infrastructures. These have evolved and diversified over time in terms of tackling relevant issues such as harmonization and standardization, but also consent practices and risk assessment. In line with the datafication, an increased use of AI-based technologies marks the current developments at the forefront of the big data research in life science and medicine that engender new issues and concerns along with opportunities. At a time when secure health data environments, such as European Health Data Space, are in the making, we argue that such meta-infrastructures can benefit both from the experience and evolution of biobanking, but also the current state of affairs in AI in medicine, regarding good governance, the social aspects and practices, as well as critical thinking about data practices, which can contribute to trustworthiness of such meta-infrastructures.
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Affiliation(s)
- Kaya Akyüz
- Department of ELSI Services and Research, BBMRI-ERIC, Graz, Austria
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5
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Assirelli E, Naldi S, Brusi V, Ciaffi J, Lisi L, Mancarella L, Pignatti F, Pulsatelli L, Faldini C, Ursini F, Neri S. Building a rheumatology biobank for reliable basic/translational research and precision medicine. Front Med (Lausanne) 2023; 10:1228874. [PMID: 37746090 PMCID: PMC10513757 DOI: 10.3389/fmed.2023.1228874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Research biobanks are non-profit structures that collect, manipulate, store, analyze and distribute systematically organized biological samples and data for research and development purposes. Over the recent years, we have established a biobank, the Rheumatology BioBank (RheumaBank) headed by the Medicine and Rheumatology unit of the IRCCS Istituto Ortopedico Rizzoli (IOR) in Bologna, Italy for the purpose of collecting, processing, storing, and distributing biological samples and associated data obtained from patients suffering from inflammatory joint diseases. RheumaBank is a research biobank, and its main objective is to promote large-scale, high-quality basic, translational, and clinical research studies that can help elucidate pathogenetic mechanisms and improve personalization of treatment choice in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and other spondyloarthritides (SpA).
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Affiliation(s)
- Elisa Assirelli
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Susanna Naldi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Veronica Brusi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Jacopo Ciaffi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lucia Lisi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luana Mancarella
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federica Pignatti
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lia Pulsatelli
- Laboratory of Immunorheumatology and Tissue Regeneration, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cesare Faldini
- 1st Orthopedic and Traumatology Department, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Francesco Ursini
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Simona Neri
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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6
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Michalska-Falkowska A, Niklinski J, Juhl H, Sulewska A, Kisluk J, Charkiewicz R, Ciborowski M, Ramlau R, Gryczka R, Piwkowski C, Kozlowski M, Miskiewicz B, Biecek P, Wnorowska K, Dzieciol-Anikiej Z, Sargsyan K, Naumnik W, Mroz R, Reszec-Gielazyn J. Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach. Cancers (Basel) 2023; 15:3742. [PMID: 37509403 PMCID: PMC10378006 DOI: 10.3390/cancers15143742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content. Molecular quality control measures included evaluating the RNA integrity number, assessing cDNA library quality and quantity, and analyzing NGS raw data. Our study yielded the creation of distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples. These workflows offer customization options to suit the capabilities of different biobanking entities. In order to ensure the appropriateness of biospecimens for advanced research applications, we introduced molecular-based quality control methods that align with the demands of high-throughput assays. The novelty of proposed workflows, rooted in innovative molecular techniques, lies in the integration of these QC methods into a comprehensive schema specifically designed for high-throughput research applications.
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Affiliation(s)
- Anna Michalska-Falkowska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Indivumed Services, 20251 Hamburg, Germany
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | | | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Robert Gryczka
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Cezary Piwkowski
- Department of Thoracic Surgery, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Borys Miskiewicz
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Karolina Wnorowska
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Paediatrics and Pediatric Neurology, Jedrzej Sniadecki Independent Public Healthcare Centre Regional Hospital, 15-278 Bialystok, Poland
| | - Zofia Dzieciol-Anikiej
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Rehabilitation, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Karine Sargsyan
- International Biobanking and Education, Medical University of Graz, 8036 Graz, Austria
- Cancer Biobank at Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Joanna Reszec-Gielazyn
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
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7
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Akyüz K, Goisauf M, Chassang G, Kozera Ł, Mežinska S, Tzortzatou-Nanopoulou O, Mayrhofer MT. Post-identifiability in changing sociotechnological genomic data environments. BIOSOCIETIES 2023:1-28. [PMID: 37359141 PMCID: PMC10042674 DOI: 10.1057/s41292-023-00299-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 03/30/2023]
Abstract
Data practices in biomedical research often rely on standards that build on normative assumptions regarding privacy and involve 'ethics work.' In an increasingly datafied research environment, identifiability gains a new temporal and spatial dimension, especially in regard to genomic data. In this paper, we analyze how genomic identifiability is considered as a specific data issue in a recent controversial case: publication of the genome sequence of the HeLa cell line. Considering developments in the sociotechnological and data environment, such as big data, biomedical, recreational, and research uses of genomics, our analysis highlights what it means to be (re-)identifiable in the postgenomic era. By showing how the risk of genomic identifiability is not a specificity of the HeLa controversy, but rather a systematic data issue, we argue that a new conceptualization is needed. With the notion of post-identifiability as a sociotechnological situation, we show how past assumptions and ideas about future possibilities come together in the case of genomic identifiability. We conclude by discussing how kinship, temporality, and openness are subject to renewed negotiations along with the changing understandings and expectations of identifiability and status of genomic data.
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Affiliation(s)
- Kaya Akyüz
- Department of Science and Technology Studies, University of Vienna, Universitätsstraße 7/Stiege II/6, Stock (NIG), 1010 Vienna, Austria
- BBMRI-ERIC, Graz, Austria
| | - Melanie Goisauf
- Department of Science and Technology Studies, University of Vienna, Universitätsstraße 7/Stiege II/6, Stock (NIG), 1010 Vienna, Austria
- BBMRI-ERIC, Graz, Austria
| | - Gauthier Chassang
- CERPOP, Université de Toulouse, Inserm, Université Paul Sabatier, Toulouse, France
- Plateforme GenoToul Societal “Ethique et Biosciences”, Toulouse, France
| | | | - Signe Mežinska
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
- BBMRI.LV, Riga, Latvia
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8
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Saginur R, Robblee JA, Vranjkovic A, Tamblyn L, Hsu A, Cooper CL, Vinh DC, Langlois MA, Crawley AM. No time for complacency: The CoVaRR-Net Biobank is an essential element of laboratory preparedness for infectious disease outbreaks. JOURNAL OF THE ASSOCIATION OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASE CANADA 2023; 8:75-84. [PMID: 37008580 PMCID: PMC10052913 DOI: 10.3138/jammi-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 03/30/2023]
Abstract
The SARS-CoV-2 pandemic highlighted the need for rapid, collaborative, and population-centric research to define health impact, develop health care policies and establish reliable diagnostic and surveillance tests. Critical for these objectives were in-depth clinical data collected in standardized fashion and large numbers of various types of human samples prior and post-viral encounter. As the pandemic evolved with the emergence of new variants of concern (VOCs), access to samples and data from infected and vaccinated individuals were needed to monitor immune durability, the possibility of increased transmissibility and virulence, and vaccine protection against new and emerging VOCs. Therefore, essential to the pandemic response is a strong laboratory and data research component, supported by effective biobanking and data sharing. Critically important to the speed of the research response is the rapid access to biobanked samples. To address critical challenges brought to light by the pandemic, the Coronavirus Variants Rapid Response Network (CoVaRR-Net), funded by the Canadian Institutes of Health Research, was established to coordinate research efforts to provide rapid evidence-based responses to emerging VOCs. The purpose of this paper is to introduce the CoVaRR-Net Biobank and define its contribution to pandemic preparedness.
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Affiliation(s)
| | | | | | - Laura Tamblyn
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Amy Hsu
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
- Bruyère Research Institute, Ottawa, Ontario, Canada
| | - Curtis L Cooper
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, Ontario, Canada
| | - Donald C Vinh
- McGill University Health Centre, Montréal, Quebec, Canada
- Research Institute-McGill University Health Centre, Montréal, Quebec, Canada
| | - Marc-André Langlois
- University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, Ontario, Canada
| | - Angela M Crawley
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
- University of Ottawa Centre for Infection, Immunity and Inflammation, Ottawa, Ontario, Canada
- Carleton University, Ottawa, Ontario, Canada
- Correspondence: Angela M Crawley, Chronic Disease Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario K1H 8L6 Canada. Telephone: 613-737-8673. E-mail:
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9
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
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10
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Swertz M, van Enckevort E, Oliveira JL, Fortier I, Bergeron J, Thurin NH, Hyde E, Kellmann A, Pahoueshnja R, Sturkenboom M, Cunnington M, Nybo Andersen AM, Marcon Y, Gonçalves G, Gini R. Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies. Yearb Med Inform 2022; 31:262-272. [PMID: 36463884 PMCID: PMC9719789 DOI: 10.1055/s-0042-1742522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVES Existing individual-level human data cover large populations on many dimensions such as lifestyle, demography, laboratory measures, clinical parameters, etc. Recent years have seen large investments in data catalogues to FAIRify data descriptions to capitalise on this great promise, i.e. make catalogue contents more Findable, Accessible, Interoperable and Reusable. However, their valuable diversity also created heterogeneity, which poses challenges to optimally exploit their richness. METHODS In this opinion review, we analyse catalogues for human subject research ranging from cohort studies to surveillance, administrative and healthcare records. RESULTS We observe that while these catalogues are heterogeneous, have various scopes, and use different terminologies, still the underlying concepts seem potentially harmonizable. We propose a unified framework to enable catalogue data sharing, with catalogues of multi-center cohorts nested as a special case in catalogues of real-world data sources. Moreover, we list recommendations to create an integrated community of metadata catalogues and an open catalogue ecosystem to sustain these efforts and maximise impact. CONCLUSIONS We propose to embrace the autonomy of motivated catalogue teams and invest in their collaboration via minimal standardisation efforts such as clear data licensing, persistent identifiers for linking same records between catalogues, minimal metadata 'common data elements' using shared ontologies, symmetric architectures for data sharing (push/pull) with clear provenance tracks to process updates and acknowledge original contributors. And most importantly, we encourage the creation of environments for collaboration and resource sharing between catalogue developers, building on international networks such as OpenAIRE and research data alliance, as well as domain specific ESFRIs such as BBMRI and ELIXIR.
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Affiliation(s)
- Morris Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands,Prof Morris Swertz Department of Genetics, HPC CB50, University Medical Center GroningenP.O. Box 30001, 9700 RB GroningenThe Netherlands
| | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Isabel Fortier
- Research Institute of the McGill University Health Center, Montreal, Canada
| | - Julie Bergeron
- Research Institute of the McGill University Health Center, Montreal, Canada
| | - Nicolas H. Thurin
- Univ. Bordeaux, INSERM CIC-P 1401, Bordeaux PharmacoEpi, Bordeaux, France
| | - Eleanor Hyde
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kellmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Miriam Sturkenboom
- Department of Datascience & Biostatistics, Julius Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | - Gonçalo Gonçalves
- Human-Centered Computing and Information Science, INESC TEC, Portugal
| | - Rosa Gini
- ARS Toscana, Florence, Italy,Correspondence to: Rosa Gini Via Dazzi 1, 55141 FlorenceItaly
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11
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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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12
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Eva G, Liese G, Stephanie B, Petr H, Leslie M, Roel V, Martine V, Sergi B, Mette H, Sarah J, Laura RM, Arnout S, Morris A S, Jan T, Xenia T, Nina V, Koert VE, Sylvie R, Greet S. Position paper on management of personal data in environment and health research in Europe. ENVIRONMENT INTERNATIONAL 2022; 165:107334. [PMID: 35696847 DOI: 10.1016/j.envint.2022.107334] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/30/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Management of datasets that include health information and other sensitive personal information of European study participants has to be compliant with the General Data Protection Regulation (GDPR, Regulation (EU) 2016/679). Within scientific research, the widely subscribed'FAIR' data principles should apply, meaning that research data should be findable, accessible, interoperable and re-usable. Balancing the aim of open science driven FAIR data management with GDPR compliant personal data protection safeguards is now a common challenge for many research projects dealing with (sensitive) personal data. In December 2020 a workshop was held with representatives of several large EU research consortia and of the European Commission to reflect on how to apply the FAIR data principles for environment and health research (E&H). Several recent data intensive EU funded E&H research projects face this challenge and work intensively towards developing solutions to access, exchange, store, handle, share, process and use such sensitive personal data, with the aim to support European and transnational collaborations. As a result, several recommendations, opportunities and current limitations were formulated. New technical developments such as federated data management and analysis systems, machine learning together with advanced search software, harmonized ontologies and data quality standards should in principle facilitate the FAIRification of data. To address ethical, legal, political and financial obstacles to the wider re-use of data for research purposes, both specific expertise and underpinning infrastructure are needed. There is a need for the E&H research data to find their place in the European Open Science Cloud. Communities using health and population data, environmental data and other publicly available data have to interconnect and synergize. To maximize the use and re-use of environment and health data, a dedicated supporting European infrastructure effort, such as the EIRENE research infrastructure within the ESFRI roadmap 2021, is needed that would interact with existing infrastructures.
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Affiliation(s)
- Govarts Eva
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium.
| | - Gilles Liese
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Bopp Stephanie
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | - Matalonga Leslie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Vermeulen Roel
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Vrijheid Martine
- ISGlobal, Barcelona, Spain; Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Beltran Sergi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Hartlev Mette
- Faculty of Law, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Standaert Arnout
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Swertz Morris A
- Department of Genetics & Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Theunis Jan
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Trier Xenia
- European Environment Agency (EEA), Copenhagen, Denmark
| | - Vogel Nina
- German Environment Agency (UBA), Berlin, Germany
| | | | - Remy Sylvie
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Schoeters Greet
- VITO Health, Flemish Institute for Technological Research (VITO), Mol, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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13
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Tarling TE, Byrne JA, Watson PH. The Availability of Human Biospecimens to Support Biomarker Research. Biomark Insights 2022; 17:11772719221091750. [PMID: 35464611 PMCID: PMC9021506 DOI: 10.1177/11772719221091750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Preserved biospecimens held in biobank inventories and clinical archives are important resources for biomarker research. Recent advances in technologies have led to an increase in use of clinical archives in particular, in order to study retrospective cohorts and to generate data relevant to tissue biomarkers. This raises the question of whether the current sizes of biobank inventories are appropriate to meet the demands of biomarker research. This commentary discusses this question by considering data concerning overall biobank and biospecimen numbers to estimate current biospecimen supply and use. The data suggests that biospecimen supply exceeds current demand. Therefore, it may be important for individual biobanks to reassess the targets for their inventories, consider culling unused portions of these inventories, and shift resources towards providing prospective custom biobanking services.
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Affiliation(s)
- Tamsin E Tarling
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, BC, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
| | - Jennifer A Byrne
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Peter H Watson
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, BC, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
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14
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Garau N, Orro A, Summers P, De Maria L, Bertolotti R, Bassis D, Minotti M, De Fiori E, Baroni G, Paganelli C, Rampinelli C. Integrating Biological and Radiological Data in a Structured Repository: a Data Model Applied to the COSMOS Case Study. J Digit Imaging 2022; 35:970-982. [PMID: 35296941 PMCID: PMC9485502 DOI: 10.1007/s10278-022-00615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
Integrating the information coming from biological samples with digital data, such as medical images, has gained prominence with the advent of precision medicine. Research in this field faces an ever-increasing amount of data to manage and, as a consequence, the need to structure these data in a functional and standardized fashion to promote and facilitate cooperation among institutions. Inspired by the Minimum Information About BIobank data Sharing (MIABIS), we propose an extended data model which aims to standardize data collections where both biological and digital samples are involved. In the proposed model, strong emphasis is given to the cause-effect relationships among factors as these are frequently encountered in clinical workflows. To test the data model in a realistic context, we consider the Continuous Observation of SMOking Subjects (COSMOS) dataset as case study, consisting of 10 consecutive years of lung cancer screening and follow-up on more than 5000 subjects. The structure of the COSMOS database, implemented to facilitate the process of data retrieval, is therefore presented along with a description of data that we hope to share in a public repository for lung cancer screening research.
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Affiliation(s)
- Noemi Garau
- Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, Italy. .,Division of Radiology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
| | - Alessandro Orro
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Paul Summers
- Division of Radiology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lorenza De Maria
- Division of Radiology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Raffaella Bertolotti
- Division of Data Management, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Danny Bassis
- School of Medicine, University of Milan, Milan, Italy
| | - Marta Minotti
- Division of Radiology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elvio De Fiori
- Division of Radiology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Guido Baroni
- Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, Italy.,Bioengineering Unit, CNAO Foundation, Pavia, Italy
| | - Chiara Paganelli
- Dipartimento Di Elettronica, Informazione E Bioingegneria, Politecnico Di Milano, Milano, Italy
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15
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Ronkainen J, Nedelec R, Atehortua A, Balkhiyarova Z, Cascarano A, Ngoc Dang V, Elhakeem A, van Enckevort E, Goncalves Soares A, Haakma S, Halonen M, Heil KF, Heiskala A, Hyde E, Jacquemin B, Keikkala E, Kerckhoffs J, Klåvus A, Kopinska JA, Lepeule J, Marazzi F, Motoc I, Näätänen M, Ribbenstedt A, Rundblad A, Savolainen O, Simonetti V, de Toro Eadie N, Tzala E, Ulrich A, Wright T, Zarei I, d’Amico E, Belotti F, Brunius C, Castleton C, Charles MA, Gaillard R, Hanhineva K, Hoek G, Holven KB, Jaddoe VWV, Kaakinen MA, Kajantie E, Kavousi M, Lakka T, Matthews J, Piano Mortari A, Vääräsmäki M, Voortman T, Webster C, Zins M, Atella V, Bulgheroni M, Chadeau-Hyam M, Conti G, Evans J, Felix JF, Heude B, Järvelin MR, Kolehmainen M, Landberg R, Lekadir K, Parusso S, Prokopenko I, de Rooij SR, Roseboom T, Swertz M, Timpson N, Ulven SM, Vermeulen R, Juola T, Sebert S. LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases. Environ Epidemiol 2022; 6:e184. [PMID: 35169663 PMCID: PMC8835657 DOI: 10.1097/ee9.0000000000000184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 11/14/2021] [Indexed: 11/29/2022] Open
Abstract
The current epidemics of cardiovascular and metabolic noncommunicable diseases have emerged alongside dramatic modifications in lifestyle and living environments. These correspond to changes in our "modern" postwar societies globally characterized by rural-to-urban migration, modernization of agricultural practices, and transportation, climate change, and aging. Evidence suggests that these changes are related to each other, although the social and biological mechanisms as well as their interactions have yet to be uncovered. LongITools, as one of the 9 projects included in the European Human Exposome Network, will tackle this environmental health equation linking multidimensional environmental exposures to the occurrence of cardiovascular and metabolic noncommunicable diseases.
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Affiliation(s)
- Justiina Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Rozenn Nedelec
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Angelica Atehortua
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Zhanna Balkhiyarova
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Bashkir State Medical University, Department of Endocrinology, Ufa, Russian Federation
| | - Anna Cascarano
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Vien Ngoc Dang
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Ahmed Elhakeem
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Esther van Enckevort
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Ana Goncalves Soares
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Sido Haakma
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Miia Halonen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Katharina F. Heil
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | - Anni Heiskala
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Eleanor Hyde
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Bénédicte Jacquemin
- University of Rennes, INSERM, School of Advanced Studies in Public Health (EHESP), Research Institute for Environmental and Occupational Health, UMR_S 1085, Rennes, France
| | - Elina Keikkala
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jules Kerckhoffs
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Anton Klåvus
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Joanna A. Kopinska
- Department of Social Sciences and Economics, Sapienza University of Rome, Rome, Italy
| | - Johanna Lepeule
- Grenoble Alpes University, INSERM, CNRS, Institute for Advanced Biosciences, Grenoble, France
| | - Francesca Marazzi
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
| | - Irina Motoc
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
| | - Mari Näätänen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Anton Ribbenstedt
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Amanda Rundblad
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Otto Savolainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Nina de Toro Eadie
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Evangelia Tzala
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Anna Ulrich
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Thomas Wright
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Iman Zarei
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | | | - Federico Belotti
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
- Department of Economics and Finance, University of Rome Tor Vergata, Rome, Italy
| | - Carl Brunius
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Marie-Aline Charles
- Center for Research in Epidemiology and Statistics, INSERM, INRAE, University of Paris, Paris, France
- Ined, INSERM, EFS, Elfe Joint Unit, Aubervilliers, France
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kati Hanhineva
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Gerard Hoek
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Kirsten B. Holven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
- National Advisory Unit on Familial Hypercholesterolemia, Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Vincent W. V. Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marika A. Kaakinen
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Eero Kajantie
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Timo Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Andrea Piano Mortari
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
| | - Marja Vääräsmäki
- Finnish Institute for Health and Welfare, Population Health Unit, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Marie Zins
- Population-based Epidemiological Cohorts Unit, INSERM UMS 11, Villejuif, France
| | - Vincenzo Atella
- CEIS Tor Vergata, Centre for Economic and International Studies, University of Rome Tor Vergata, Rome, Italy
- Department of Economics and Finance, University of Rome Tor Vergata, Rome, Italy
- Stanford University, Stanford, CA
| | | | - Marc Chadeau-Hyam
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Gabriella Conti
- Department of Economics, University College London, London, United Kingdom
- Social Research Institute, London, United Kingdom
| | - Jayne Evans
- Beta Technology Ltd, Doncaster, United Kingdom
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Barbara Heude
- Center for Research in Epidemiology and Statistics, INSERM, INRAE, University of Paris, Paris, France
| | - Marjo-Riitta Järvelin
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St. Mary’s Hospital, London, United Kingdom
| | - Marjukka Kolehmainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karim Lekadir
- Artificial Intelligence in Medicine Lab (BCN-AIM), University of Barcelona, Barcelona, Spain
- Department of Mathematics and Computer Science, University of Barcelona, Barcelona, Spain
| | | | - Inga Prokopenko
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- UMR 8199-EGID, Institut Pasteur de Lille, CNRS, University of Lille, Lille, France
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Susanne R. de Rooij
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
| | - Tessa Roseboom
- Amsterdam UMC, Epidemiology and Data Science, University of Amsterdam, Amsterdam Public Health, Amsterdam, the Netherlands
- Gynaecology and Obstetrics, Amsterdam Reproduction and Development Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Morris Swertz
- Department of Genetics and Genomics Coordination Center, University of Groningen, Groningen, the Netherlands
| | - Nicholas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, United Kingdom
| | - Stine M. Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Blindern, Oslo, Norway
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
- Julius Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Teija Juola
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- Corresponding Author. Address: Faculty of Medicine, Center for Life Course Health Research, University of Oulu, PO Box 5000, FIN-90014, Finland. E-mail: (S. Sebert)
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Freeberg MA, Fromont LA, D’Altri T, Romero AF, Ciges J, Jene A, Kerry G, Moldes M, Ariosa R, Bahena S, Barrowdale D, Barbero M, Fernandez-Orth D, Garcia-Linares C, Garcia-Rios E, Haziza F, Juhasz B, Llobet O, Milla G, Mohan A, Rueda M, Sankar A, Shaju D, Shimpi A, Singh B, Thomas C, de la Torre S, Uyan U, Vasallo C, Flicek P, Guigo R, Navarro A, Parkinson H, Keane T, Rambla J. The European Genome-phenome Archive in 2021. Nucleic Acids Res 2022; 50:D980-D987. [PMID: 34791407 PMCID: PMC8728218 DOI: 10.1093/nar/gkab1059] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/08/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource.
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Affiliation(s)
- Mallory Ann Freeberg
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren A Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Teresa D’Altri
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Anna Foix Romero
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Jorge Izquierdo Ciges
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Aina Jene
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Giselle Kerry
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Mauricio Moldes
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Roberto Ariosa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Silvia Bahena
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Daniel Barrowdale
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Marcos Casado Barbero
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Dietmar Fernandez-Orth
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Carles Garcia-Linares
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Emilio Garcia-Rios
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Frédéric Haziza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Bela Juhasz
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Oscar Martinez Llobet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Gemma Milla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Anand Mohan
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Aravind Sankar
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Dona Shaju
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Ashutosh Shimpi
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Babita Singh
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Coline Thomas
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabela de la Torre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Umuthan Uyan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Claudia Vasallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Paul Flicek
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Helen Parkinson
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Thomas Keane
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
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17
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Akyüz K, Chassang G, Goisauf M, Kozera Ł, Mezinska S, Tzortzatou O, Mayrhofer MT. Biobanking and risk assessment: a comprehensive typology of risks for an adaptive risk governance. LIFE SCIENCES, SOCIETY AND POLICY 2021; 17:10. [PMID: 34903285 PMCID: PMC8666836 DOI: 10.1186/s40504-021-00117-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/01/2021] [Indexed: 05/03/2023]
Abstract
Biobanks act as the custodians for the access to and responsible use of human biological samples and related data that have been generously donated by individuals to serve the public interest and scientific advances in the health research realm. Risk assessment has become a daily practice for biobanks and has been discussed from different perspectives. This paper aims to provide a literature review on risk assessment in order to put together a comprehensive typology of diverse risks biobanks could potentially face. Methodologically set as a typology, the conceptual approach used in this paper is based on the interdisciplinary analysis of scientific literature, the relevant ethical and legal instruments and practices in biobanking to identify how risks are assessed, considered and mitigated. Through an interdisciplinary mapping exercise, we have produced a typology of potential risks in biobanking, taking into consideration the perspectives of different stakeholders, such as institutional actors and publics, including participants and representative organizations. With this approach, we have identified the following risk types: economic, infrastructural, institutional, research community risks and participant's risks. The paper concludes by highlighting the necessity of an adaptive risk governance as an integral part of good governance in biobanking. In this regard, it contributes to sustainability in biobanking by assisting in the design of relevant risk management practices, where they are not already in place or require an update. The typology is intended to be useful from the early stages of establishing such a complex and multileveled biomedical infrastructure as well as to provide a catalogue of risks for improving the risk management practices already in place.
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Affiliation(s)
- Kaya Akyüz
- BBMRI-ERIC, Graz, Austria.
- Department of Science and Technology Studies, University of Vienna, Vienna, Austria.
| | - Gauthier Chassang
- BBMRI-ERIC, Graz, Austria
- CERPOP, Université de Toulouse, Inserm, Université Paul Sabatier, Toulouse, France
| | - Melanie Goisauf
- BBMRI-ERIC, Graz, Austria
- Department of Science and Technology Studies, University of Vienna, Vienna, Austria
| | | | - Signe Mezinska
- BBMRI-ERIC, Graz, Austria
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Olga Tzortzatou
- BBMRI-ERIC, Graz, Austria
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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18
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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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19
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The Dutch National TissueArchive Portal enables efficient, consistent, and transparent procurement of diagnostic tissue samples for scientific use. Cell Tissue Bank 2021; 22:727-736. [PMID: 34432159 PMCID: PMC8558151 DOI: 10.1007/s10561-021-09949-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/25/2021] [Indexed: 11/30/2022]
Abstract
Biobanks play a crucial role in enabling biomedical research by facilitating scientific use of valuable human biomaterials. The PALGA foundation—a nationwide network and registry of histo- and cytopathology in the Netherlands—was established to promote the provision of data within and between pathology departments, and to make the resulting knowledge available for healthcare. Apart from the pathology data, we aimed to utilize PALGA’s nationwide network to find and access the rich wealth of Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples for scientific use.
We implemented the Dutch National TissueArchive Portal (DNTP) to utilize PALGA’s nationwide network for requesting FFPE tissue samples. The DNTP consists of (1) a centrally organized internet portal to improve the assessing, processing, harmonization, and monitoring of the procurement process, while (2) dedicated HUB-employees provide practical support at peripheral pathology departments. Since incorporation of the DNTP, both the number of filed requests for FFPE tissue samples and the amount of HUB-mediated support increased 55 and 29% respectively. In line, the sample procurement duration time decreased significantly (− 47%). These findings indicate that implementation of the DNTP improved the frequency, efficiency, and transparency of FFPE tissue sample procurement for research in the Netherlands. To conclude, the need for biological resources is growing persistently to enable precision medicine. Here, we access PALGA’s national, pathology network by implementation of the DNTP to allow for efficient, consistent, and transparent exchange of FFPE tissue samples for research across the Netherlands.
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20
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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: 56] [Impact Index Per Article: 18.7] [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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21
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Eder J, Shekhovtsov VA. Data quality for federated medical data lakes. INTERNATIONAL JOURNAL OF WEB INFORMATION SYSTEMS 2021. [DOI: 10.1108/ijwis-03-2021-0026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
Medical research requires biological material and data collected through biobanks in reliable processes with quality assurance. Medical studies based on data with unknown or questionable quality are useless or even dangerous, as evidenced by recent examples of withdrawn studies. Medical data sets consist of highly sensitive personal data, which has to be protected carefully and is available for research only after the approval of ethics committees. The purpose of this research is to propose an architecture to support researchers to efficiently and effectively identify relevant collections of material and data with documented quality for their research projects while observing strict privacy rules.
Design/methodology/approach
Following a design science approach, this paper develops a conceptual model for capturing and relating metadata of medical data in biobanks to support medical research.
Findings
This study describes the landscape of biobanks as federated medical data lakes such as the collections of samples and their annotations in the European federation of biobanks (Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium, BBMRI-ERIC) and develops a conceptual model capturing schema information with quality annotation. This paper discusses the quality dimensions for data sets for medical research in-depth and proposes representations of both the metadata and data quality documentation with the aim to support researchers to effectively and efficiently identify suitable data sets for medical studies.
Originality/value
This novel conceptual model for metadata for medical data lakes has a unique focus on the high privacy requirements of the data sets contained in medical data lakes and also stands out in the detailed representation of data quality and metadata quality of medical data sets.
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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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23
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The landscape of biobanks in Poland-characteristics of Polish biobanking units at the beginning of BBMRI.pl organization. J Transl Med 2021; 19:267. [PMID: 34158056 PMCID: PMC8218293 DOI: 10.1186/s12967-021-02926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/04/2021] [Indexed: 12/01/2022] Open
Abstract
Background Biobanking is an area of scientific activity that is growing in strength and importance. The variety of collections combining biological samples and medical scientific information makes biobanking an indispensable tool in the development of modern medicine. In 2016, Poland, a country with one of the largest populations in Europe, joined the Biobanking and BioMolecular resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) to facilitate access to quality-defined human disease-relevant biological resources. This push led to the development of the Polish Biobanking Network. The purpose of this paper is to present the current state of biobanks in Poland in the context of their location, nature and resources. Methods To obtain information about and overall characteristics of Polish entities dealing with biobanking biological material, the dedicated Information Survey was designed. The survey was prepared in an electronic form and consisted of 53 questions—both open and closed, single and multiple choice—with some questions depending on each other. Sixty-five Polish biobanks/biorepositories participated in the survey. Results Polish biobanks are mostly affiliated with research entities (universities—42% and research institutes—30%). The data collected indicate that a considerable number of Polish biobanks are specialized (33 units), in contrast to population-based biobanks (8 units). These biobanks are mostly focused on collecting samples from oncological (23 biobanks) and rare diseases (12 biobanks). In general, great diversity was found in the material collected. Scientists working in Polish biobanks are very open to scientific cooperation (declared by 60% of units) and sharing their collections with the international scientific environment. In terms of quality issues, most biobanks declared that their quality management system was in the process of implementation (45%) or had already been implemented (23%). Conclusions Although biobanking in Poland is still in its infancy, the results of this study seem promising and may be valuable to the wider biobanking research community. The distribution of biobanks throughout the Polish territory, their connection with scientific and clinical units, and their involvement in research on rare diseases may contribute to an increase in the number of multicenter studies.
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Scapicchio C, Gabelloni M, Forte SM, Alberich LC, Faggioni L, Borgheresi R, Erba P, Paiar F, Marti-Bonmati L, Neri E. DICOM-MIABIS integration model for biobanks: a use case of the EU PRIMAGE project. Eur Radiol Exp 2021; 5:20. [PMID: 33977357 PMCID: PMC8113005 DOI: 10.1186/s41747-021-00214-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
PRIMAGE is a European Commission-financed project dealing with medical imaging and artificial intelligence aiming to create an imaging biobank in oncology. The project includes a task dedicated to the interoperability between imaging and standard biobanks. We aim at linking Digital imaging and Communications in Medicine (DICOM) metadata to the Minimum Information About BIobank data Sharing (MIABIS) standard of biobanking. A very first integration model based on the fusion of the two existing standards, MIABIS and DICOM, has been developed. The fundamental method was that of expanding the MIABIS core to the imaging field, adding DICOM metadata derived from CT scans of 18 paediatric patients with neuroblastoma. The model was developed with the relational database management system Structured Query Language. The integration data model has been built as an Entity Relationship Diagram, commonly used to organise data within databases. Five additional entities have been linked to the “Image Collection” subcategory in order to include the imaging metadata more specific to the particular type of data: Body Part Examined, Modality Information, Dataset Type, Image Analysis, and Registration Parameters. The model is a starting point for the expansion of MIABIS with further DICOM metadata, enabling the inclusion of imaging data in biorepositories.
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Affiliation(s)
- Camilla Scapicchio
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
| | - Michela Gabelloni
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sara Maria Forte
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Leonor Cerdá Alberich
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Valencia, Spain
| | - Lorenzo Faggioni
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Rita Borgheresi
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Paola Erba
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Fabiola Paiar
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luis Marti-Bonmati
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group (GIBI230), La Fe University and Polytechnic Hospital and Health Research Institute, Valencia, Spain
| | - Emanuele Neri
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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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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26
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Matzke LA, Watson PH. Biobanking for Cancer Biomarker Research: Issues and Solutions. Biomark Insights 2020; 15:1177271920965522. [PMID: 33192050 PMCID: PMC7594219 DOI: 10.1177/1177271920965522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Biomarkers are critical tools that underpin precision medicine. However there has been slow progress and frequent failure of biomarker development. The root causes are multifactorial. Here, we focus on the need for fast, efficient, and reliable access to quality biospecimens as a critical area that impacts biomarker development. We discuss the past history of biobanking and the evolution of biobanking processes relevant to the specific area of cancer biomarker development as an example, and describe some solutions that can improve this area, thus potentially accelerating biomarker research.
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Affiliation(s)
- Lise A Matzke
- Office of Biobank Education and
Research, Department of Pathology and Laboratory Medicine, University of British
Columbia, Vancouver, British Columbia, Canada
- Biobanking and Biospecimen Research
Services, Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia,
Canada
| | - Peter H Watson
- Office of Biobank Education and
Research, Department of Pathology and Laboratory Medicine, University of British
Columbia, Vancouver, British Columbia, Canada
- Biobanking and Biospecimen Research
Services, Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia,
Canada
- Canadian Tissue Repository Network,
Vancouver, Canada
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27
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Kozera L, Kuliczkowski W, Gocek E. Cardiovascular risk and metabolic profile of Polish citizens from Lower Silesia. First signs of metabolic crisis? Arch Med Sci 2020; 18:617-623. [PMID: 35591838 PMCID: PMC9102627 DOI: 10.5114/aoms.2020.99922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/14/2019] [Indexed: 11/17/2022] Open
Abstract
Introduction Population biobanks are essential for the development of public health screening and improvement of personalized medicine. Since 2012, Biobank of Łukasiewicz Research Network - PORT Polish Center for Technology Development (PORT Biobank) has collected more than 120 000 biological samples from nearly 5000 inhabitants of Lower Silesia, together with a variety of demographic, anthropometric, life style and health information. Material and methods The analyzed group consisted of 2274 participants (1398 women, 876 men). Both women and men were further subdivided into five age decades (20+, 30+, 40+, 50+, 60+). For this study, the level of lipids (total cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglycerides) was estimated and correlated with the level of high-sensitivity C-reactive protein (hs-CRP) and biometric parameters. Results We have demonstrated for the first time that biochemical changes that may lead to cardiovascular diseases (CVD) occurred already in the group of people aged 30+. Our observation is based on measurements of lipids, glucose, inflammatory (hs-CRP) and biometric markers such as body mass index (BMI) and waist-to-hip ratio (WHR). Conclusions Positive correlations with age for these variables suggest the ongoing progress of metabolic changes, which in the end may lead to a fatal outcome such as myocardial infarction or stroke. It suggests that CVD screening programs should be dedicated to a wider group, especially younger citizens, in order to prevent fatal outcomes related to CVD.
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Affiliation(s)
- Lukasz Kozera
- Łukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
- BBMRI.pl
| | - Wiktor Kuliczkowski
- BBMRI.pl
- Department and Clinic of Cardiology, Wroclaw Medical University, Wroclaw, Poland
| | - Elzbieta Gocek
- Łukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
- BBMRI.pl
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Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management. Curr Opin Biotechnol 2020; 65:45-51. [DOI: 10.1016/j.copbio.2019.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
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Haslacher H, Bayer M, Fiegl H, Gerner M, Hofer P, Korb M, Neururer S, Perkmann T, Plattner K, Sargsyan K, Steiner E, Stumptner C, Walter I, Wieser M, Wutte A, Wagner O, Zatloukal K. Quality management at the national biobanking level - establishing a culture of mutual trust and support: the BBMRI.at example. Clin Chem Lab Med 2020; 57:e301-e305. [PMID: 31188755 DOI: 10.1515/cclm-2019-0491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 11/15/2022]
Affiliation(s)
- Helmuth Haslacher
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Heidelinde Fiegl
- Department of Obstetrics and Gynaecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Marlene Gerner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Philipp Hofer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Melanie Korb
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sabrina Neururer
- Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Perkmann
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | | | - Eberhard Steiner
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Cornelia Stumptner
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ingrid Walter
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Monika Wieser
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Oswald Wagner
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Kurt Zatloukal
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
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Catchpoole DR, Florindi F, Ahern C, Garcia DL, Mullins P, Van Enckevort E, Zaayenga A, Mayrhofer MT, Holub P. Expanding the BBMRI-ERIC Directory into a Global Catalogue of COVID-19-Ready Collections: A Joint Initiative of BBMRI-ERIC and ISBER. Biopreserv Biobank 2020; 18:479-480. [PMID: 32936006 DOI: 10.1089/bio.2020.29075.drc] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniel R Catchpoole
- Tumour Bank, CCRU, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | | | | | | | - Piper Mullins
- Pan-Smithsonian Cryo-Initiative, Washington, District of Columbia, USA
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Speirs V, Foden H, Hair J, Tate R, Pitman H, Oien K, Hall A, Thomas G. The Cellular and Molecular Pathology Biobanking Sample Quality Improvement Tool: A Guide for Improving the Quality of Tissue Collections for Biomedical Research and Clinical Trials in Cancer. Biopreserv Biobank 2020; 19:86-90. [PMID: 32936002 DOI: 10.1089/bio.2020.0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Valerie Speirs
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Harriet Foden
- National Cancer Research Institute, London, United Kingdom
| | - Jane Hair
- Greater Glasgow and Clyde Biorepository, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Raffaella Tate
- Patient Advocate, NCRI Consumer Forum, London, United Kingdom
| | - Helen Pitman
- National Cancer Research Institute, London, United Kingdom
| | - Karin Oien
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew Hall
- Independent Medical Research Advocate, Newcastle, United Kingdom
| | - Gareth Thomas
- Faculty of Medicine Cancer Sciences Unit, Southampton University, Southampton, United Kingdom
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N-Glycome changes reflecting resistance to platinum-based chemotherapy in ovarian cancer. J Proteomics 2020; 230:103964. [PMID: 32898699 DOI: 10.1016/j.jprot.2020.103964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022]
Abstract
A number of studies have reported aberrant glycosylation in connection with malignancy. Our investigation further expands on this topic through the examination of N-glycans, which could be associated with the resistance of advanced stage, high-grade non-mucinous ovarian cancer to platinum/taxane based chemotherapy. We used tissue samples of 83 ovarian cancer patients, randomly divided into two independent cohorts (basic and validation). Both groups involved either cases with/without postoperative tumor residue or the cases determined either resistant or sensitive to this chemotherapy. In the validation cohort, preoperative serum samples were also available. N-glycans released from tumors and sera were permethylated and analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The MS analysis yielded a consecutive detection of 68 (tissue) and 63 (serum) N-glycan spectral signals. Eight of these were found to be differentially abundant in tissues of both independent cohorts including the cases with a postoperative cancer residue. One of these glycans was detected as differentially abundant in sera of the validation cohort. No statistically significant differences in intensities due to the same N-glycans were found in the cases without postoperative macroscopic residues in either the basic or validation cohort. From the biochemical point of view, the statistically significant N-glycans correspond to the structures carrying bisecting (terminal) GlcNAc residue and tetra-antennary structures with sialic acid and/or fucose residues. Among them, six tissue N-glycans could be considered potential markers connected with a resistance to chemotherapy in ovarian cancer patients. The prediction of primary resistance to standard chemotherapy may identify the group of patients suitable for alternative treatment strategies. SIGNIFICANCE: Drug resistance has become a major impediment to a successful treatment of patients with advanced ovarian cancer. The glycomic measurements related to cancer are becoming increasingly popular in identification of the key molecules as potential diagnostic and prognostic indicators. Our report deals with identification of differences in N-glycosylation of proteins in tissue and serum samples from the individuals showing sensitivity or resistance to platinum/taxane-based chemotherapy. The detection sensitivity to chemotherapy is vitally important for these patients.
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Schüttler C, Huth V, von Jagwitz-Biegnitz M, Lablans M, Prokosch HU, Griebel L. A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study. J Med Internet Res 2020; 22:e17739. [PMID: 32663150 PMCID: PMC7463387 DOI: 10.2196/17739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/24/2020] [Accepted: 06/14/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. OBJECTIVE To ensure the sustainable use of such a tool, we included researchers as participants in an end user-based usability evaluation. METHODS To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. RESULTS Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). CONCLUSIONS The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.
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Affiliation(s)
- Christina Schüttler
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Verena Huth
- German Biobank Node, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,University Medical Center Mannheim, Mannheim, Germany
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lena Griebel
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Jaddoe VWV, Felix JF, Andersen AMN, Charles MA, Chatzi L, Corpeleijn E, Donner N, Elhakeem A, Eriksson JG, Foong R, Grote V, Haakma S, Hanson M, Harris JR, Heude B, Huang RC, Inskip H, Järvelin MR, Koletzko B, Lawlor DA, Lindeboom M, McEachan RRC, Mikkola TM, Nader JLT, de Moira AP, Pizzi C, Richiardi L, Sebert S, Schwalber A, Sunyer J, Swertz MA, Vafeiadi M, Vrijheid M, Wright J, Duijts L. The LifeCycle Project-EU Child Cohort Network: a federated analysis infrastructure and harmonized data of more than 250,000 children and parents. Eur J Epidemiol 2020; 35:709-724. [PMID: 32705500 PMCID: PMC7387322 DOI: 10.1007/s10654-020-00662-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022]
Abstract
Early life is an important window of opportunity to improve health across the full lifecycle. An accumulating body of evidence suggests that exposure to adverse stressors during early life leads to developmental adaptations, which subsequently affect disease risk in later life. Also, geographical, socio-economic, and ethnic differences are related to health inequalities from early life onwards. To address these important public health challenges, many European pregnancy and childhood cohorts have been established over the last 30 years. The enormous wealth of data of these cohorts has led to important new biological insights and important impact for health from early life onwards. The impact of these cohorts and their data could be further increased by combining data from different cohorts. Combining data will lead to the possibility of identifying smaller effect estimates, and the opportunity to better identify risk groups and risk factors leading to disease across the lifecycle across countries. Also, it enables research on better causal understanding and modelling of life course health trajectories. The EU Child Cohort Network, established by the Horizon2020-funded LifeCycle Project, brings together nineteen pregnancy and childhood cohorts, together including more than 250,000 children and their parents. A large set of variables has been harmonised and standardized across these cohorts. The harmonized data are kept within each institution and can be accessed by external researchers through a shared federated data analysis platform using the R-based platform DataSHIELD, which takes relevant national and international data regulations into account. The EU Child Cohort Network has an open character. All protocols for data harmonization and setting up the data analysis platform are available online. The EU Child Cohort Network creates great opportunities for researchers to use data from different cohorts, during and beyond the LifeCycle Project duration. It also provides a novel model for collaborative research in large research infrastructures with individual-level data. The LifeCycle Project will translate results from research using the EU Child Cohort Network into recommendations for targeted prevention strategies to improve health trajectories for current and future generations by optimizing their earliest phases of life.
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Affiliation(s)
- Vincent W V Jaddoe
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands. .,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Janine F Felix
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne-Marie Nybo Andersen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France.,ELFE Joint Unit, French Institute for Demographic Studies (Ined), French Institute for Medical Research and Health (INSERM), French Blood Agency, Aubervilliers, France
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nina Donner
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Ahmed Elhakeem
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore.,Singapore Institute for Clinical Sciences (SICS), Agency for Science and Technology (A*STAR), Singapore, Singapore
| | - Rachel Foong
- Telethon Kids Institute, Perth, WA, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, WA, Australia
| | - Veit Grote
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Sido Haakma
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Mark Hanson
- Institute of Developmental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jennifer R Harris
- Centre for Fertility and Health, The Norwegian Institute of Public Health, Oslo, Norway.,Division of Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | | | - Hazel Inskip
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Marjo-Riitta Järvelin
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK.,Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Berthold Koletzko
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Maarten Lindeboom
- Department of Economics, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosemary R C McEachan
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | | | - Johanna L T Nader
- Department of Genetics and Bioinformatics, Division of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Angela Pinot de Moira
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Costanza Pizzi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sylvain Sebert
- Center for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ameli Schwalber
- Concentris Research Management GmbH, Fürstenfeldbruck, Germany
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marina Vafeiadi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, The Generation R Study Group, (Na 29-18), PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Pavlenko E, Strech D, Langhof H. Implementation of data access and use procedures in clinical data warehouses. A systematic review of literature and publicly available policies. BMC Med Inform Decis Mak 2020; 20:157. [PMID: 32652989 PMCID: PMC7353743 DOI: 10.1186/s12911-020-01177-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/02/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The promises of improved health care and health research through data-intensive applications rely on a growing amount of health data. At the core of large-scale data integration efforts, clinical data warehouses (CDW) are also responsible for data governance, managing data access and (re)use. As the complexity of the data flow increases, greater transparency and standardization of criteria and procedures are required in order to maintain objective oversight and control. Therefore, the development of practice oriented and evidence-based policies is crucial. This study assessed the spectrum of data access and use criteria and procedures in clinical data warehouses governance internationally. METHODS We performed a systematic review of (a) the published scientific literature on CDW and (b) publicly available information on CDW data access, e.g., data access policies. A qualitative thematic analysis was applied to all included literature and policies. RESULTS Twenty-three scientific publications and one policy document were included in the final analysis. The qualitative analysis led to a final set of three main thematic categories: (1) requirements, including recipient requirements, reuse requirements, and formal requirements; (2) structures and processes, including review bodies and review values; and (3) access, including access limitations. CONCLUSIONS The description of data access and use governance in the scientific literature is characterized by a high level of heterogeneity and ambiguity. In practice, this might limit the effective data sharing needed to fulfil the high expectations of data-intensive approaches in medical research and health care. The lack of publicly available information on access policies conflicts with ethical requirements linked to principles of transparency and accountability. CDW should publicly disclose by whom and under which conditions data can be accessed, and provide designated governance structures and policies to increase transparency on data access. The results of this review may contribute to the development of practice-oriented minimal standards for the governance of data access, which could also result in a stronger harmonization, efficiency, and effectiveness of CDW.
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Affiliation(s)
- Elena Pavlenko
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- QUEST - Center for Transforming Biomedical Research, Charité - University Medicine, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany
| | - Daniel Strech
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- QUEST - Center for Transforming Biomedical Research, Charité - University Medicine, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany
| | - Holger Langhof
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- QUEST - Center for Transforming Biomedical Research, Charité - University Medicine, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany.
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany.
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36
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Eklund N, Andrianarisoa NH, van Enckevort E, Anton G, Debucquoy A, Müller H, Zaharenko L, Engels C, Ebert L, Neumann M, Geeraert J, T'Joen V, Demski H, Caboux É, Proynova R, Parodi B, Mate S, van Iperen E, Merino-Martinez R, Quinlan PR, Holub P, Silander K. Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events. Biopreserv Biobank 2020; 18:155-164. [PMID: 32302498 PMCID: PMC7310316 DOI: 10.1089/bio.2019.0129] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: The Minimum Information About BIobank data Sharing (MIABIS) was initiated in 2012. MIABIS aims to create a common biobank terminology to facilitate data sharing in biobanks and sample collections. The MIABIS Core terminology consists of three components describing biobanks, sample collections, and studies, in which information on samples and sample donors is provided at aggregated form. However, there is also a need to describe samples and sample donors at an individual level to allow more elaborate queries on available biobank samples and data. Therefore the MIABIS terminology has now been extended with components describing samples and sample donors at an individual level. Materials and Methods: The components were defined according to specific scope and use cases by a large group of experts, and through several cycles of reviews, according to the new MIABIS governance model of BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium). The guiding principles applied in developing these components included the following terms: model should consider only samples of human origin, model should be applicable to all types of samples and all sample donors, and model should describe the current status of samples stored in a given biobank. Results: A minimal set of standard attributes for defining samples and sample donors is presented here. We added an "event" component to describe attributes that are not directly describing samples or sample donors but are tightly related to them. To better utilize the generic data model, we suggest a procedure by which interoperability can be promoted, using specific MIABIS profiles. Discussion: The MIABIS sample and donor component extensions and the new generic data model complement the existing MIABIS Core 2.0 components, and substantially increase the potential usability of this terminology for better describing biobank samples and sample donors. They also support the use of individual level data about samples and sample donors to obtain accurate and detailed biobank availability queries.
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Affiliation(s)
- Niina Eklund
- THL Biobank, Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Esther van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Heimo Müller
- Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | | | | | | | - Michael Neumann
- Interdisciplinary Bank of Biomaterials and Data Würzburg, University Hospital Würzburg, Würzburg, Germany
| | - Joachim Geeraert
- Faculty of Medicine and Health Sciences, University of Ghent/University Hospital Ghent, Ghent, Belgium
| | - Veronique T'Joen
- Faculty of Medicine and Health Sciences, University of Ghent/University Hospital Ghent, Ghent, Belgium
| | - Hans Demski
- Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | | | - Sebastian Mate
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Erik van Iperen
- Amsterdam UMC Biobank, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | | | - Philip R Quinlan
- Digital Research Service, University of Nottingham, Nottingham, United Kingdom
| | | | - Kaisa Silander
- THL Biobank, Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
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37
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Future-proofing biobanks' governance. Eur J Hum Genet 2020; 28:989-996. [PMID: 32424324 PMCID: PMC7468350 DOI: 10.1038/s41431-020-0646-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/27/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
Good biobank governance implies—at a minimum—transparency and accountability and the implementation of oversight mechanisms. While the biobanking community is in general committed to such principles, little is known about precisely which governance strategies biobanks adopt to meet those objectives. We conducted an exploratory analysis of governance mechanisms adopted by research biobanks, including genetic biobanks, located in Europe and Canada. We reviewed information available on the websites of 69 biobanks, and directly contacted them for additional information. Our study identified six types of commonly adopted governance strategies: communication, compliance, expert advice, external review, internal procedures, and partnerships. Each strategy is implemented through different mechanisms including, independent ethics assessment, informed consent processes, quality management, data access control, legal compliance, standard operating procedures and external certification. Such mechanisms rely on a wide range of bodies, committees and actors from both within and outside the biobanks themselves. We found that most biobanks aim to be transparent about their governance mechanisms, but could do more to provide more complete and detailed information about them. In particular, the retrievable information, while showing efforts to ensure biobanks operate in a legitimate way, does not specify in sufficient detail how governance mechanisms support accountability, nor how they ensure oversight of research operations. This state of affairs can potentially undermine biobanks’ trustworthiness to stakeholders and the public in a long-term perspective. Given the ever-increasing reliance of biomedical research on large biological repositories and their associated databases, we recommend that biobanks increase their efforts to future-proof their governance.
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Meinung B, Martin D, Zimmermann U. Standardization in biobanking – between cooperation and competition. J LAB MED 2019. [DOI: 10.1515/labmed-2019-0105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This article presents the current situation of German biobanks and shows future fields of action in the European and international context on the basis of upcoming legal and normative challenges. It gives an overview of the development of the international biobank standard ISO 20387 and the commitment of German biobank experts in the ISO committee TC276. Less attention than the biobank standard per se has so far been paid to the basic mechanisms by which standards are developed and the potential of their application and accreditation. In this sense, this article deals with the motivation for active participation in standardization projects. We discuss the status of ISO 20387 as a conformity assessment standard and the consequence of accreditation as a performance monitor.
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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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Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, Scollen S. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat Rev Genet 2019; 20:693-701. [PMID: 31455890 PMCID: PMC7115898 DOI: 10.1038/s41576-019-0156-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.
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Affiliation(s)
- Gary Saunders
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Regina Becker
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, Luxembourg
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'Enfants de la Timone, Marseille, France
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cath Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Søren Brunak
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peter Goodhand
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jaap Heringa
- Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands
| | | | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Nick Juty
- School of Computer Science, The University of Manchester, Manchester, UK
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Brane Leskosek
- IBMI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | | | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Steven Newhouse
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bengt Persson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala, Sweden
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jordi Rambla
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | - Morris A Swertz
- BBMRI-NL/University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Pg., Barcelona, Spain
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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Linsen L, Vanhees K, Vanoppen E, Ulenaers K, Driessens S, Penders J, Somers V, Stinissen P, Rummens JL. Raising to the Challenge: Building a Federated Biobank to Accelerate Translational Research-The University Biobank Limburg. Front Med (Lausanne) 2019; 6:224. [PMID: 31750305 PMCID: PMC6842921 DOI: 10.3389/fmed.2019.00224] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
Irreproducibility of research results is one of the major contributing factors to the failure of translating basic research results into tangible bedside progress. To address this, the University Biobank Limburg (UBiLim) was founded by a collaboration between Hasselt University, the Hospital East-Limburg, and the Jessa Hospital. This paper describes the evolution of this process and the barriers encountered on the way. UBiLim evolved from an archival collection over a single-site biobank into a federated structure, supporting translational research at the founding institutions. Currently, UBiLim is a federated biobank, with an established organizational structure and processing, and storage facilities at each of the three sites. All activities are integrated in an ISO15189-accredited Quality Management System and based on (inter)national biobank guidelines. Common methods for processing and storage of a plethora of sample types, suitable for state-of-the-art applications, were validated and implemented. Because the biobank is embedded in two hospitals, the request of researchers to include certain sample types or enroll specific patient groups can quickly be met. Funding has been a major challenge in each step of its evolution and remains the biggest issue for long-term biobank sustainability. To a lesser extent, the Belgian legislation and the operational cost of information management system are also concerns for smooth biobank operations. Nonetheless, UBiLim serves as a facilitator and accelerator for translational research in the Limburg area of Belgium that, given the fields of research, may have an impact on international patient care.
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Affiliation(s)
- Loes Linsen
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Limburg Clinical Research Center, Hasselt University, Diepenbeek, Belgium.,Clinical Laboratory, Jessa Hospital, Hasselt, Belgium
| | - Kimberly Vanhees
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Limburg Clinical Research Center, Hasselt University, Diepenbeek, Belgium.,Clinical Laboratory, Jessa Hospital, Hasselt, Belgium
| | - Evi Vanoppen
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Clinical Laboratory, Jessa Hospital, Hasselt, Belgium
| | - Kim Ulenaers
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Suzanne Driessens
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Clinical Laboratory, Hospital East-Limburg (ZOL), Genk, Belgium
| | - Joris Penders
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Limburg Clinical Research Center, Hasselt University, Diepenbeek, Belgium.,Clinical Laboratory, Hospital East-Limburg (ZOL), Genk, Belgium
| | - Veerle Somers
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Piet Stinissen
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Jean-Luc Rummens
- University Biobank Limburg (UBiLim), Hasselt, Belgium.,Faculty of Medicine and Life Sciences, Limburg Clinical Research Center, Hasselt University, Diepenbeek, Belgium.,Clinical Laboratory, Jessa Hospital, Hasselt, Belgium
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Vesterinen T, Salmenkivi K, Mustonen H, Kuopio T, Lappi-Blanco E, Paavonen T, Vainio P, Knuuttila A, Carpén O, Haglund C, Arola J. Performance of Finnish biobanks in nationwide pulmonary carcinoid tumour research. Virchows Arch 2019; 476:273-283. [PMID: 31385069 PMCID: PMC7028842 DOI: 10.1007/s00428-019-02625-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
Finnish hospital-integrated biobanks administer millions of formalin-fixed paraffin-embedded tissue samples collected within the clinical diagnostics. According to the Finnish Biobank Act, these samples can be coupled with patients' clinical follow-up data and the data retrieved from national health registries. We collected a nationwide pulmonary carcinoid tumour series from Finnish biobanks to study prognostic factors as well as to explore how the number of tumours found in the Finnish biobanks corresponds to the number of tumours registered by the Finnish Cancer Registry (FCR). Finnish biobanks identified 88% of the tumours registered by the FCR and were able to deliver 63%. The main reasons for lacking samples were paucity of resected primary tumour tissue, incompatible primary diagnosis, and the absence of tissue blocks in the archives. The main bottleneck in the sample application process was retrieving patient data. Altogether, we received 224 tumour samples with appropriate patient data and identified six prognostic factors for shorter disease-specific survival: age over 56 years at the time of diagnosis, tumour size over 2.5 cm, atypical histology, Ki-67 proliferation index higher than 2.5%, hilar/mediastinal lymph node involvement at the time of diagnosis, and the presence of metastatic disease. In conclusion, the Finnish biobank infrastructure offers excellent opportunities for tissue-based research. However, to be able to develop the biobank operations further, involving more medical knowledge in the sample and data acquisition process is a necessity. Also, when working with tissue samples collected over decades, histological expertise is essential for re-evaluation and re-classification of the samples.
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Affiliation(s)
- Tiina Vesterinen
- HUSLAB, Department of Pathology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, Helsinki, Finland.
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Tukholmankatu 8, Helsinki, Finland.
| | - Kaisa Salmenkivi
- HUSLAB, Department of Pathology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, Helsinki, Finland
| | - Harri Mustonen
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, Helsinki, Finland
| | - Teijo Kuopio
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, Jyväskylä, Finland
- Department of Pathology, Central Finland Health Care District, Keskussairaalantie 19, Jyväskylä, Finland
| | - Elisa Lappi-Blanco
- Department of Pathology, Center for Cancer Research and Translational Medicine, Oulu University Hospital and University of Oulu, Aapistie 5, Oulu, Finland
| | - Timo Paavonen
- Department of Pathology, Fimlab Laboratories and Department of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, Finland
| | - Paula Vainio
- Department of Pathology, University of Turku and Turku University Hospital, Kiinamyllynkatu 4-8, Turku, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, Heart and Lung Center, and Cancer Center, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, Helsinki, Finland
| | - Olli Carpén
- HUSLAB, Department of Pathology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, Helsinki, Finland
- Research Program in Systems Oncology, University of Helsinki, Haartmaninkatu 8, Helsinki, Finland
| | - Caj Haglund
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, Helsinki, Finland
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki, Finland
| | - Johanna Arola
- HUSLAB, Department of Pathology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 3, Helsinki, Finland
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Vamathevan J, Apweiler R, Birney E. Biomolecular Data Resources: Bioinformatics Infrastructure for Biomedical Data Science. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Technological advances have continuously driven the generation of bio-molecular data and the development of bioinformatics infrastructure, which enables data reuse for scientific discovery. Several types of data management resources have arisen, such as data deposition databases, added-value databases or knowledgebases, and biology-driven portals. In this review, we provide a unique overview of the gradual evolution of these resources and discuss the goals and features that must be considered in their development. With the increasing application of genomics in the health care context and with 60 to 500 million whole genomes estimated to be sequenced by 2022, biomedical research infrastructure is transforming, too. Systems for federated access, portable tools, provision of reference data, and interpretation tools will enable researchers to derive maximal benefits from these data. Collaboration, coordination, and sustainability of data resources are key to ensure that biomedical knowledge management can scale with technology shifts and growing data volumes.
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Affiliation(s)
- Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, der Sloot KWJ V, Peters V, Van Dullemen HM, Visschedijk MC, EAM F, Swertz MA, Dijkstra G, Weersma RK. The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol 2019; 19:5. [PMID: 30621600 PMCID: PMC6325838 DOI: 10.1186/s12876-018-0917-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients. CONSTRUCTION AND CONTENT We initiated the 1000IBD project ( https://1000ibd.org ) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing. UTILITY AND DISCUSSION All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive ( https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models. CONCLUSIONS We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.
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Affiliation(s)
- Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K. J. Van der Velde
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. D. Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - A. Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - V. Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - L. M. Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Van der Sloot KWJ
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - V. Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - H. M. Van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - M. C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - Festen EAM
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. A. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - G. Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - R. K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
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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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Langhof H, Kahrass H, Illig T, Jahns R, Strech D. Current practices for access, compensation, and prioritization in biobanks. Results from an interview study. Eur J Hum Genet 2018; 26:1572-1581. [PMID: 30089824 DOI: 10.1038/s41431-018-0228-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
Human biological materials and related data stored in biobanks are valuable resources for biomedical research. Transparent, effective, and efficient governance structures and procedures for access, compensation, and priority setting are needed, but recent debates indicate challenges in the practical application of such governance processes. This study aimed to assess the practical experiences and attitudes of biobank experts regarding the governance of biosample access, prioritization, and compensation. Qualitative, semi-structured telephone interviews were conducted with 20 biobank directors from eight countries. Respondents highlighted the need for sound governance structures in order to ensure acceptance by all stakeholders (patients/donors, researchers, research funders, public, and others). They stressed practical difficulties in trying to make best use of biomaterials. As biobanks often form part of larger academic and clinical settings, the different and sometimes conflicting interests of researchers, clinicians, patients, funders, and biobank staff currently affect the governance of access decisions. Investments such as intellectual input, financial, and human resources need to be compensated adequately. Biobanks thereby have a dual role stewarding the hosted biosamples and acting as a service provider for local researchers from universities or hospitals. In order to facilitate efficient use of human biological materials, greater harmonization of at least minimum standards for access and compensation are required at both a national and an international level.
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Affiliation(s)
- Holger Langhof
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany.
| | - Hannes Kahrass
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School (MHH), Hannover, Germany
| | - Roland Jahns
- University Hospital of Wuerzburg, Interdisciplinary Bank of Biomaterials and Data Wuerzburg (ibdw), Wuerzburg, Germany
| | - Daniel Strech
- Institute for History, Ethics and Philosophy of Medicine, Hannover Medical School (MHH), Hannover, Germany.,Charité - University Medicine Berlin, QUEST - Center for Transforming Biomedical Research, Berlin Institute of Health (BIH), Berlin, Germany
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Kongsholm NCH, Christensen ST, Hermann JR, Larsen LA, Minssen T, Pedersen LB, Rajam N, Tommerup N, Tupasela A, Schovsbo J. Challenges for the Sustainability of University-Run Biobanks. Biopreserv Biobank 2018; 16:312-321. [DOI: 10.1089/bio.2018.0054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
| | - Søren Tvorup Christensen
- Section of Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Janne Rothmar Hermann
- Center for Advanced Studies in Biomedical Innovation Law (CeBIL), University of Copenhagen, Copenhagen, Denmark
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Timo Minssen
- Center for Advanced Studies in Biomedical Innovation Law (CeBIL), University of Copenhagen, Copenhagen, Denmark
| | - Lotte Bang Pedersen
- Section of Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Neethu Rajam
- Center for Information and Innovation Law (CIIR), University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Aaro Tupasela
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Schovsbo
- Center for Information and Innovation Law (CIIR), University of Copenhagen, Copenhagen, Denmark
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Boeckhout M, Zielhuis GA, Bredenoord AL. The FAIR guiding principles for data stewardship: fair enough? Eur J Hum Genet 2018; 26:931-936. [PMID: 29777206 PMCID: PMC6018669 DOI: 10.1038/s41431-018-0160-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/27/2018] [Indexed: 11/09/2022] Open
Abstract
The FAIR guiding principles for research data stewardship (findability, accessibility, interoperability, and reusability) look set to become a cornerstone of research in the life sciences. A critical appraisal of these principles in light of ongoing discussions and developments about data sharing is in order. The FAIR principles point the way forward for facilitating data sharing more systematically-provided that a number of ethical, methodological, and organisational challenges are addressed as well.
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Affiliation(s)
- Martin Boeckhout
- Julius Center for Health Sciences and Primary Care, Department of Medical Humanities, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Gerhard A Zielhuis
- Parelsnoer Institute, Utrecht, The Netherlands
- Radboud Biobank, Radboud university medical center, Nijmegen, The Netherlands
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands
| | - Annelien L Bredenoord
- Julius Center for Health Sciences and Primary Care, Department of Medical Humanities, University Medical Center Utrecht, Utrecht, The Netherlands
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49
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Paradiso AV, Daidone MG, Canzonieri V, Zito A. Biobanks and scientists: supply and demand. J Transl Med 2018; 16:136. [PMID: 29783984 PMCID: PMC5963141 DOI: 10.1186/s12967-018-1505-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/05/2018] [Indexed: 02/07/2023] Open
Abstract
The biobanks, providers of biospecimens, and the scientists, users of biological material, are both strategic actors in translational medicine but the communication about those two subjects seems to be delicate. Recently, biobank managers from US and Europe stressed the danger of underuse of biospecimens stored in their biobanks thus stimulating the debate about innovative ways to collect samples and to communicate their availability. We hypothesize that the already stored collections meet the interest of present scientists only in specific situations. Serial biospecimens from patients with large associated clinical data concerning voluptuary habits, environmental exposure, anthropomorphic information are needed to meet the even more specific projects the scientists are planning. The hypothesis of activation of specific sections in ranked journals aimed to facilitate the communication between partners interested in finding/collecting ad hoc biospecimens is discussed.
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Affiliation(s)
- Angelo Virgilio Paradiso
- Oncologia Medica Indirizzo Sperimentale & Direzione Biobanca, Istituto Tumori G Paolo II, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Bari, Italy.
| | - Maria Grazia Daidone
- Department Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto NazionaleTumori, Milan, Italy
| | - Vincenzo Canzonieri
- Pathology Unit and Biobank, Centro Riferimento Oncologico (CRO), IRCCS, National Cancer Institute, Aviano, Italy
| | - Alfredo Zito
- Pathology Unit, Istituto Tumori G Paolo II, IRCCS, Bari, Italy
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50
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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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