51
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Biobanking 3.0: evidence based and customer focused biobanking. Clin Biochem 2014; 47:300-8. [PMID: 24406300 DOI: 10.1016/j.clinbiochem.2013.12.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/08/2013] [Accepted: 12/13/2013] [Indexed: 01/19/2023]
Abstract
Biobanking is a new and very dynamic field. To achieve long term financial sustainability of biobank infrastructures we propose that a new focus is needed on activities, products and services provided by the biobank that relate to the external stakeholder: biobanking 3.0. Earlier stages of biobanking are biobanking 1.0 (primary focus on the number of biospecimens and data) and biobanking 2.0 (primary focus on the quality of biospecimens and data). Both stages 1.0 and 2.0 are predominantly product oriented areas and have required a mostly internal focus on operational development within the biobank itself. In this paper we will introduce our concept of biobanking 3.0 which capitalizes on the earlier stages but dictates a shift in focus to enhancing the value and impact for the three major sets of external stakeholders (people/patients, funders, and research customers) and creating a path to balanced and planned investment in biobank infrastructure and the sustainability of biobanking. Biobanking 3.0 will improve real understanding as well as perceptions of value across different stakeholders. Patients and donors will appreciate seeing how their biospecimens and data are effectively used for research. Funders will value the ability to plan efficient targeting of funding and to monitor the impact of their support. Researchers will capitalize on the ability to translate their ideas into effective knowledge. Ultimately adoption of biobanking 3.0 will impact on the sustainability in the three main dimensions relevant to biobanking: social sustainability (acceptability), operational sustainability (efficiency), and financial sustainability (accomplishment).
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52
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Schubert W. Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems. J Mol Recognit 2014; 27:3-18. [PMID: 24375580 PMCID: PMC4283051 DOI: 10.1002/jmr.2326] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023]
Abstract
Understanding biological systems at the level of their relational (emergent) molecular properties in functional protein networks relies on imaging methods, able to spatially resolve a tissue or a cell as a giant, non-random, topologically defined collection of interacting supermolecules executing myriads of subcellular mechanisms. Here, the development and findings of parameter-unlimited functional super-resolution microscopy are described-a technology based on the fluorescence imaging cycler (IC) principle capable of co-mapping thousands of distinct biomolecular assemblies at high spatial resolution and differentiation (<40 nm distances). It is shown that the subcellular and transcellular features of such supermolecules can be described at the compositional and constitutional levels; that the spatial connection, relational stoichiometry, and topology of supermolecules generate hitherto unrecognized functional self-segmentation of biological tissues; that hierarchical features, common to thousands of simultaneously imaged supermolecules, can be identified; and how the resulting supramolecular order relates to spatial coding of cellular functionalities in biological systems. A large body of observations with IC molecular systems microscopy collected over 20 years have disclosed principles governed by a law of supramolecular segregation of cellular functionalities. This pervades phenomena, such as exceptional orderliness, functional selectivity, combinatorial and spatial periodicity, and hierarchical organization of large molecular systems, across all species investigated so far. This insight is based on the high degree of specificity, selectivity, and sensitivity of molecular recognition processes for fluorescence imaging beyond the spectral resolution limit, using probe libraries controlled by ICs.
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Affiliation(s)
- Walter Schubert
- Molecular pattern recognition research group, O-v-G-university MagdeburgGermany
- International faculty, Max-Planck (CAS-MPG) partner institute for computational biologyShanghai, China
- Human toponome project, TNLMunich, Germany
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53
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54
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Landegren U. Offshoots of the ESF functional genomics programme. N Biotechnol 2013; 30:296-8. [PMID: 23295551 DOI: 10.1016/j.nbt.2012.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022]
Abstract
After the conclusion of the second five-year period of the European Science Foundation (ESF) programme on functional genomics, it is time to take stock and evaluate its accomplishments. The programme networked leading scientists from a large number of European countries for strategy discussions about the promotion of functional genomics research, and to arrange scientific meetings and exchange programmes. In brief, I believe this programme has punched above its weight, and that it has successfully contributed to the overall organisation of molecular biosciences in Europe. With a modest annual budget the programme has created several interesting new opportunities, some of which may have yet to show their full impact. However, these mini-reviews are intended to provide a personal perspective on this functional genomics effort, and accordingly I focus on my personal experiences from the ESF programme.
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Affiliation(s)
- Ulf Landegren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjoldsväg 20, SE-75185 Uppsala, Sweden.
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55
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Mischak H, Ioannidis JPA, Argiles A, Attwood TK, Bongcam-Rudloff E, Broenstrup M, Charonis A, Chrousos GP, Delles C, Dominiczak A, Dylag T, Ehrich J, Egido J, Findeisen P, Jankowski J, Johnson RW, Julien BA, Lankisch T, Leung HY, Maahs D, Magni F, Manns MP, Manolis E, Mayer G, Navis G, Novak J, Ortiz A, Persson F, Peter K, Riese HH, Rossing P, Sattar N, Spasovski G, Thongboonkerd V, Vanholder R, Schanstra JP, Vlahou A. Implementation of proteomic biomarkers: making it work. Eur J Clin Invest 2012; 42:1027-36. [PMID: 22519700 PMCID: PMC3464367 DOI: 10.1111/j.1365-2362.2012.02674.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
While large numbers of proteomic biomarkers have been described, they are generally not implemented in medical practice. We have investigated the reasons for this shortcoming, focusing on hurdles downstream of biomarker verification, and describe major obstacles and possible solutions to ease valid biomarker implementation. Some of the problems lie in suboptimal biomarker discovery and validation, especially lack of validated platforms with well-described performance characteristics to support biomarker qualification. These issues have been acknowledged and are being addressed, raising the hope that valid biomarkers may start accumulating in the foreseeable future. However, successful biomarker discovery and qualification alone does not suffice for successful implementation. Additional challenges include, among others, limited access to appropriate specimens and insufficient funding, the need to validate new biomarker utility in interventional trials, and large communication gaps between the parties involved in implementation. To address this problem, we propose an implementation roadmap. The implementation effort needs to involve a wide variety of stakeholders (clinicians, statisticians, health economists, and representatives of patient groups, health insurance, pharmaceutical companies, biobanks, and regulatory agencies). Knowledgeable panels with adequate representation of all these stakeholders may facilitate biomarker evaluation and guide implementation for the specific context of use. This approach may avoid unwarranted delays or failure to implement potentially useful biomarkers, and may expedite meaningful contributions of the biomarker community to healthcare.
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Affiliation(s)
- Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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56
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Kozlakidis Z, Mant C, Cason J. Bridging the Financial Gap Through Providing Contract Services: A Model for Publicly Funded Clinical Biobanks. Biopreserv Biobank 2012; 10:357-60. [DOI: 10.1089/bio.2012.0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Zisis Kozlakidis
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, United Kingdom
- The King's College London Infectious Diseases BioBank, The National Institute of Health Research's Comprehensive Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Christine Mant
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, United Kingdom
| | - John Cason
- Department of Infectious Diseases, King's College London, Guy's Hospital, London, United Kingdom
- The King's College London Infectious Diseases BioBank, The National Institute of Health Research's Comprehensive Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
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57
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Hens K, Van El CE, Borry P, Cambon-Thomsen A, Cornel MC, Forzano F, Lucassen A, Patch C, Tranebjaerg L, Vermeulen E, Salvaterra E, Tibben A, Dierickx K. Developing a policy for paediatric biobanks: principles for good practice. Eur J Hum Genet 2012; 21:2-7. [PMID: 22713814 PMCID: PMC3533257 DOI: 10.1038/ejhg.2012.99] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The participation of minors in biobank research can offer great benefits for science and
health care. However, as minors are a vulnerable population they are also in need of
adequate protective measures when they are enrolled in research. Research using biobanked
biological samples from children poses additional ethical issues to those raised by
research using adult biobanks. For example, small children have only limited capacity, if
any, to understand the meaning and implications of the research and to give a documented
agreement to it. Older minors are gradually acquiring this capacity. We describe
principles for good practice related to the inclusion of minors in biobank research,
focusing on issues related to benefits and subsidiarity, consent, proportionality and
return of results. Some of these issues are currently heavily debated, and we conclude by
providing principles for good practice for policy makers of biobanks, researchers and
anyone involved in dealing with stored tissue samples from children. Actual implementation
of the principles will vary according to different jurisdictions.
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Affiliation(s)
- Kristien Hens
- Health, Ethics and Society, Maastricht University, Maastricht, The Netherlands.
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Hobbs A, Starkbaum J, Gottweis U, Wichmann HE, Gottweis H. The privacy-reciprocity connection in biobanking: comparing German with UK strategies. Public Health Genomics 2012; 15:272-84. [PMID: 22722691 DOI: 10.1159/000336671] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In recent years, the adequacy of the 'gift' model of research participation has been increasingly questioned. This study used focus groups to explore how potential and actual participants of biobanks in the UK and Germany negotiate the relationship between concerns over privacy protection, reciprocity and benefit sharing. In Germany, 15 focus groups (n = 151) were conducted: 11 general public groups (n = 116) and 4 with former cohort study participants including the KORA and the Popgen cohort study (n = 35). In the UK, 9 focus groups (n = 61) were conducted: 4 general public groups (n = 33) and 5 with UK Biobank and European Huntington's Disease (Euro-HD) Registry biorepository participants (n = 28). Forms of reciprocity were found to partially mitigate potential and actual biobank participants' concerns over personal privacy risks and future unintended consequences of biobank in both Germany and the UK. Specifically, notions of individual reciprocity were at the forefront in the context of personal disadvantages to participation, while communal reciprocity was prominent when potential and actual participants were discussing the uncertainty of the long-term nature of biobanking. The research indicates that reciprocity can be viewed as a mode to deal with individuals' concerns about participating in a biobank, both by acting as a return 'favor' or 'gift,' and through establishing an ongoing relationship between participants, researchers and society. It is suggested that future biobanking projects will need to flexibly combine individual and communal forms of reciprocity if they are to recruit and maintain sufficient numbers of participants.
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Affiliation(s)
- A Hobbs
- Science and Technology Studies Unit, Department of Sociology, University of York, York, UK
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59
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Landegren U, Vänelid J, Hammond M, Nong RY, Wu D, Ullerås E, Kamali-Moghaddam M. Opportunities for sensitive plasma proteome analysis. Anal Chem 2012; 84:1824-30. [PMID: 22248085 DOI: 10.1021/ac2032222] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite great interest, investments, and efforts, the ongoing search for plasma protein biomarkers for disease so far has come up surprisingly empty-handed. Although discovery programs have revealed large numbers of biomarker candidates, the clinical utility has been validated for only a very small number of these. While this disappointing state of affairs may suggest that plasma protein biomarkers have little more to offer for diagnostics, we take the perspective that experimental conditions might not have been optimal and that analyses will be required that offer far greater sensitivity than currently available, in terms of numbers of molecules needed for unambiguous detection. Accordingly, techniques are needed to search deep and wide for protein biomarker candidates. The requirements and feasibility of such assays will be discussed.
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Affiliation(s)
- Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, The Rudbeck Laboratory, 75185 Uppsala, Sweden.
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60
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Eder J, Gottweis H, Zatloukal K. IT Solutions for Privacy Protection in Biobanking. Public Health Genomics 2012; 15:254-62. [DOI: 10.1159/000336663] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Schubert W, Gieseler A, Krusche A, Serocka P, Hillert R. Next-generation biomarkers based on 100-parameter functional super-resolution microscopy TIS. N Biotechnol 2011; 29:599-610. [PMID: 22209707 DOI: 10.1016/j.nbt.2011.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 12/06/2011] [Accepted: 12/12/2011] [Indexed: 01/25/2023]
Abstract
Functional super-resolution (fSR) microscopy is based on the automated toponome imaging system (TIS). fSR-TIS provides insight into the myriad of different cellular functionalities by direct imaging of large subcellular protein networks in morphologically intact cells and tissues, referred to as the toponome. By cyclical fluorescence imaging of at least 100 molecular cell components, fSR-TIS overcomes the spectral limitations of fluorescence microscopy, which is the essential condition for the detection of protein network structures in situ/in vivo. The resulting data sets precisely discriminate between cell types, subcellular structures, cell states and diseases (fSR). With up to 16 bits per protein, the power of combinatorial molecular discrimination (PCMD) is at least 2(100) per subcellular data point. It provides the dimensionality necessary to uncover thousands of distinct protein clusters including their subcellular hierarchies controlling protein network topology and function in the one cell or tissue section. Here we review the technology and findings showing that functional protein networks of the cell surface in different cancers encompass the same hierarchical and spatial coding principle, but express cancer-specific toponome codes within that scheme (referred to as TIS codes). Findings suggest that TIS codes, extracted from large-scale toponome data, have the potential to be next-generation biomarkers because of their cell type and disease specificity. This is functionally substantiated by the observation that blocking toponome-specific lead proteins results in disassembly of molecular networks and loss of function.
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Affiliation(s)
- Walter Schubert
- Molecular Pattern Recognition Research Group, Medical Faculty, Otto-von-Guericke-University Magdeburg, Germany.
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