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Meredith AJ, Simeon-Dubach D, Matzke LA, Cheah S, Watson PH. Biospecimen Data Reporting in the Research Literature. Biopreserv Biobank 2019; 17:326-333. [DOI: 10.1089/bio.2018.0143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Anna J. Meredith
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Lise A. Matzke
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stefanie Cheah
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Peter H. Watson
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Tumour Tissue Repository, Deeley Research Centre, BC Cancer Agency, Victoria, Canada
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T'Joen V, Vaneeckhaute L, Priem S, Van Woensel S, Bekaert S, Berneel E, Van Der Straeten C. Rationalized Development of a Campus-Wide Cell Line Dataset for Implementation in the Biobank LIMS System at Bioresource Center Ghent. Front Med (Lausanne) 2019; 6:137. [PMID: 31294023 PMCID: PMC6603147 DOI: 10.3389/fmed.2019.00137] [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: 03/28/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
The Bioresource center Ghent is the central hospital-integrated biobank of Ghent University Hospital. Our mission is to facilitate translational biomedical research by collecting, storing and providing high quality biospecimens to researchers. Several of our biobank partners store large amounts of cell lines. As cell lines are highly important both in basic research and preclinical screening phases, good annotation, authentication, and quality of these cell lines is pivotal in translational biomedical science. A Biobank Information Management System (BIMS) was implemented as sample and data management system for human bodily material. The samples are annotated by the use of defined datasets, based on the BRISQ (Biospecimen Reporting for Improved Study Quality) and Minimum Information About Biobank data Sharing (MIABIS) guidelines completed with SPREC (Standard PREanalytical Coding) information. However, the defined dataset for human bodily material is not ideal to capture the specific cell line data. Therefore, we set out to develop a rationalized cell line dataset. Through comparison of different datasets of online cell banks (human, animal, and stem cell), we established an extended cell line dataset of 156 data fields that was further analyzed until a smaller dataset—the survey dataset of 54 data fields—was obtained. The survey dataset was spread throughout our campus to all cell line users to rationalize the fields of the dataset and their potential use. Analysis of the survey data revealed only small differences in preferences in data fields between human, animal, and stem cell lines. Hence, one essential dataset for human, animal and stem cell lines was compiled consisting of 33 data fields. The essential dataset was prepared for implementation in our BIMS system. Good Clinical Data Management Practices formed the basis of our decisions in the implementation phase. Known standards, reference lists and ontologies (such as ICD-10-CM, animal taxonomy, cell line ontology…) were considered. The semantics of the data fields were clearly defined, enhancing the data quality of the stored cell lines. Therefore, we created an essential cell line dataset with defined data fields, useable for multiple cell line users.
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Affiliation(s)
- Veronique T'Joen
- Bioresource Center Ghent, Health, Innovation and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Lieven Vaneeckhaute
- Data Management Unit, Health, Innovation and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Sara Priem
- Bioresource Center Ghent, Health, Innovation and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Steven Van Woensel
- Bioresource Center Ghent, Health, Innovation and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Sofie Bekaert
- Department of Public Health and Primary Care, Faculty for Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Berneel
- Bioresource Center Ghent, Health, Innovation and Research Center, Ghent University Hospital, Ghent, Belgium
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Szarvas T, Nyirády P, Ogawa O, Furuya H, Rosser CJ, Kobayashi T. Urinary Protein Markers for the Detection and Prognostication of Urothelial Carcinoma. Methods Mol Biol 2018; 1655:251-273. [PMID: 28889391 DOI: 10.1007/978-1-4939-7234-0_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bladder cancer diagnosis and surveillance is mainly based on cystoscopy and urine cytology. However, both methods have significant limitations; urine cytology has a low sensitivity for low-grade tumors, while cystoscopy is uncomfortable for the patients. Therefore, in the last decade urine analysis was the subject of intensive research resulting in the identification of many potential biomarkers for the detection, surveillance, or prognostic stratification of bladder cancer. Current trends move toward the development of multiparametric models to improve the diagnostic accuracy compared with single molecular markers. Recent technical advances for high-throughput and more sensitive measurements have led to the development of multiplex assays showing potential for more efficient tools toward future clinical application. In this review, we focus on the findings of urinary protein research in the context of detection and prognostication of bladder cancer. Furthermore, we provide an up-to-date overview on the recommendations for the quality evaluation of published studies as well as for the conduction of future urinary biomarker studies.
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Affiliation(s)
- Tibor Szarvas
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary.
| | - Péter Nyirády
- Department of Urology, Semmelweis University, Üllői út 78/b 1082, Budapest, Hungary
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideki Furuya
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Charles J Rosser
- Clinical and Translational Research Program, University of Hawaii Cancer Center, 701 Ilalo St, Rm 327, Honolulu, HI, 96813, USA
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Benson EE, Harding K, Mackenzie-dodds J. A new quality management perspective for biodiversity conservation and research: Investigating Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) using Natural History Museum and culture collections as case studies. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1201167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Erica E. Benson
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Keith Harding
- Damar Research Scientists, Damar, Drum Road, Cuparmuir, Fife, Scotland KY15 5RJ, UK
| | - Jacqueline Mackenzie-dodds
- Molecular Collections, Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Rush A, Byrne JA. Quality and reporting practices in an Australian cancer biobank cohort. Clin Biochem 2016; 49:492-497. [DOI: 10.1016/j.clinbiochem.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/16/2022]
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Nussbeck SY, Rabone M, Benson EE, Droege G, Mackenzie-Dodds J, Lawlor RT. "Life in Data"--Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data. Biopreserv Biobank 2016; 14:56-64. [PMID: 26808538 PMCID: PMC4761830 DOI: 10.1089/bio.2015.0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Clinical, biodiversity, and environmental biobanks share many data standards, but there is a lack of harmonization on how data are defined and used among biobank fields. This article reports the outcome of an interactive, multidisciplinary session at a meeting of the European, Middle Eastern, and African Society for Biopreservation and Biobanking (ESBB) designed to encourage a 'learning-from-each-other' approach to achieve consensus on data needs and data management across biobank communities. MATERIALS, METHODS, AND RESULTS The Enviro-Bio and ESBBperanto Working Groups of the ESBB co-organized an interactive session at the 2013 conference (Verona, Italy), presenting data associated with biobanking processes, using examples from across different fields. One-hundred-sixty (160) diverse biobank participants were provided electronic voting devices with real-time screen display of responses to questions posed during the session. The importance of data standards and robust data management was recognized across the conference cohort, along with the need to raise awareness about these issues within and across different biobank sectors. DISCUSSION AND CONCLUSION While interactive sessions require a commitment of time and resources, and must be carefully coordinated for consistency and continuity, they stimulate the audience to be pro-active and direct the course of the session. This effective method was used to gauge opinions about significant topics across different biobanking communities. The votes revealed the need to: (a) educate biobanks in the use of data management tools and standards, and (b) encourage a more cohesive approach for how data and samples are tracked, exchanged, and standardized across biobanking communities. Recommendations for future interactive sessions are presented based on lessons learned.
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Affiliation(s)
- Sara Y. Nussbeck
- Department of Medical Informatics and UMG Biobank, University Medical Center Göttingen, Göttingen, Germany
| | - Muriel Rabone
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Erica E. Benson
- Damar Research Scientists, Cuparmuir, Fife, Scotland, United Kingdom
| | - Gabriele Droege
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | | | - Rita T. Lawlor
- ARC-Net Applied Research on Cancer Centre, University of Verona, Verona, Italy
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Herpel E, Schmitt S, Kiehntopf M. Qualität von Biomaterialien im Biobanking von Flüssig- und Gewebeproben. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:325-35. [PMID: 26753866 DOI: 10.1007/s00103-015-2294-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Esther Herpel
- Pathologisches Institut, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
- Gewebebank des Nationalen Centrums für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Sabrina Schmitt
- Gewebebank des Nationalen Centrums für Tumorerkrankungen (NCT), Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Michael Kiehntopf
- Institut für Klinische Chemie und Laboratoriumsdiagnostik, Universitätsklinikum Jena, Jena, Deutschland.
- Integrierte Biobank Jena (IBBJ), Universitätsklinikum Jena, Jena, Deutschland.
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A critical analysis of cancer biobank practices in relation to biospecimen quality. Biophys Rev 2015; 7:369-378. [PMID: 28510101 DOI: 10.1007/s12551-015-0178-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 12/26/2022] Open
Abstract
There are concerns that a substantial proportion of published research data is not reproducible, which may partially explain the frequent failure to translate pre-clinical results to clinical care. High-quality cancer biospecimens are needed for robust, reproducible research findings, with most researchers obtaining these specimens from cancer biobanks or tumour banks. This review provides an overview of the types of quality control (QC) activities conducted within cancer biobanks that pertain to biospecimen quality and of biospecimen quality reporting tools, including SPREC and BRISQ. We examine how QC assay results and other biospecimen data are communicated from biobanks to researchers, and whether these activities lead to improved biospecimen quality reporting within the literature and/or to improved research outcomes. We also discuss operational factors that limit QC activities within biobanks and evidence gaps requiring further research. In summary, whereas the provision of quality biospecimens is a common aim of cancer biobanks, QC activities remain underreported and are rarely discussed in the literature, compared with other aspects of biobank operations. Further research is required to determine how biobanks can most efficiently optimise biospecimen quality, and how communication between biobanks and researchers can be improved.
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Abstract
INTRODUCTION Biobanking refers to the infrastructure, policies and practices involved in collecting, processing, storing and disseminating biological samples. Biospecimen methods research to support biobanking through evidence-based practices is now recognized as critical to the success of biobanking and translational research. SOURCES OF DATA Data concerning biospecimen research have appeared in the literature for many years, primarily in journals and textbooks focused on clinical chemistry, epidemiology and pathology. Recently, new efforts have been initiated to support the development of evidence-based biobanking practices. AREAS OF AGREEMENT Generally, researchers who are engaged in studies involving biospecimen collection are aware of the effects of pre-analytical variables on their downstream analyses, and they normally take steps to control those variables to publish reproducible results. Knowledge of such biospecimen research data is often unknown in the clinical setting unless the researchers are engaged in a project requiring strict protocols. AREAS OF CONTROVERSY There is broad agreement of the need to develop evidence-based practices to achieve consistent quality for biospecimens and data. However, due to inconsistencies in the literature, there is some disagreement on whether biospecimens need to be collected according to a 'platinum' standard or local biobank standards for collecting samples as 'fit-for-purpose' will be sufficient. GROWING POINTS New and expanded efforts, on an international basis where possible, need to be developed to better harmonize biospecimen management practices. AREAS TIMELY FOR DEVELOPING RESEARCH Additional biospecimen methods research leading to the development of evidence-based practices is critical to translational research and personalized medicine.
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Affiliation(s)
- Jim Vaught
- International Society for Biological and Environmental Repositories, Kensington, MD, USA
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