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Bettio V, Mazzucco E, Aleni C, Cracas S, Rinaldi C, Antona A, Varalda M, Venetucci J, Ferrante D, Rimedio A, Capello D. UPO Biobank: The Challenge of Integrating Biobanking into the Academic Environment to Support Translational Research. J Pers Med 2023; 13:911. [PMID: 37373900 DOI: 10.3390/jpm13060911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Biobanks are driving motors of precision and personalized medicine by providing high-quality biological material/data through the standardization and harmonization of their collection, preservation, and distribution. UPO Biobank was established in 2020 as an institutional, disease, and population biobank within the University of Piemonte Orientale (UPO) for the promotion and support of high-quality, multidisciplinary studies. UPO Biobank collaborates with UPO researchers, sustaining academic translational research, and supports the Novara Cohort Study, a longitudinal cohort study involving the population in the Novara area that will collect data and biological specimens that will be available for epidemiological, public health, and biological studies on aging. UPO Biobank has been developed by implementing the quality standards for the field and the ethical and legal issues and normative about privacy protection, data collection, and sharing. As a member of the "Biobanking and Biomolecular Resources Research Infrastructure" (BBMRI) network, UPO Biobank aims to expand its activity worldwide and launch cooperation with new national and international partners and researchers. The objective of this manuscript is to report an institutional and operational experience through the description of the technical and procedural solutions and ethical and scientific implications associated with the establishment of this university research biobank.
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Affiliation(s)
- Valentina Bettio
- UPO Biobank, University of Piemonte Orientale, 28100 Novara, Italy
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Eleonora Mazzucco
- UPO Biobank, University of Piemonte Orientale, 28100 Novara, Italy
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Chiara Aleni
- Department of Sustainable Development and Ecological Transition, University of Piemonte Orientale, 13100 Vercelli, Italy
| | - Silvia Cracas
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Carmela Rinaldi
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
- Learning and Research Area, A.O.U. Maggiore della Carità, 28100 Novara, Italy
| | - Annamaria Antona
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marco Varalda
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Jacopo Venetucci
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Daniela Ferrante
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Antonio Rimedio
- Ethics Committee of the University "Hospital Major of Charity" in Novara, Local Health Authorities Biella, 28100 Novara, Italy
| | - Daniela Capello
- UPO Biobank, University of Piemonte Orientale, 28100 Novara, Italy
- Department of Translational Medicine, Center of Excellence in Aging Sciences, University of Piemonte Orientale, 28100 Novara, Italy
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Janzen W, Admirand E, Andrews J, Boeckeler M, Jayakody C, Majer C, Porwal G, Sana S, Unkuri S, Zaayenga A. Establishing and Maintaining a Robust Sample Management System. SLAS Technol 2019; 24:256-268. [PMID: 30865569 DOI: 10.1177/2472630319834471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper has been written by the SLAS Sample Management Special Interest Group to serve as a guide to the best practices and methods in establishing and maintaining a high-quality sample management system. The topics covered are applicable to sample types ranging from small molecules to biologics to tissue samples. It has been put together using the collective experience of the authors in start-up companies, small pharma, agricultural research, IT, academia, biorepositories, and large pharma companies. Our hope is that sharing our experience will streamline the process of setting up a new sample management system and help others avoid some of the problems that we have encountered.
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Abstract
Sample automation and management is increasingly important as the number and size of population-scale and high-throughput projects grow. This is particularly the case in large-scale population studies where sample size is far outpacing the commonly used 96-well plate format. To facilitate management and transfer of samples in this format, we present Samasy, a web-based application for the construction of a sample database, intuitive display of sample and batch information, and facilitation of automated sample transfer or subset. Samasy is designed with ease-of-use in mind, can be quickly set up, and runs in any web browser.
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Heinle CE, Gaultier NPE, Miller D, Purbojati RW, Lauro FM. MetaLIMS, a simple open-source laboratory information management system for small metagenomic labs. Gigascience 2017; 6:1-6. [PMID: 28430964 PMCID: PMC5449644 DOI: 10.1093/gigascience/gix025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/15/2017] [Accepted: 03/26/2017] [Indexed: 11/14/2022] Open
Abstract
Background As the cost of sequencing continues to fall, smaller groups increasingly initiate and manage larger sequencing projects and take on the complexity of data storage for high volumes of samples. This has created a need for low-cost laboratory information management systems (LIMS) that contain flexible fields to accommodate the unique nature of individual labs. Many labs do not have a dedicated information technology position, so LIMS must also be easy to setup and maintain with minimal technical proficiency. MetaLIMS is a free and open-source web-based application available via GitHub. The focus of MetaLIMS is to store sample metadata prior to sequencing and analysis pipelines. Initially designed for environmental metagenomics labs, in addition to storing generic sample collection information and DNA/RNA processing information, the user can also add fields specific to the user's lab. MetaLIMS can also produce a basic sequencing submission form compatible with the proprietary Clarity LIMS system used by some sequencing facilities. To help ease the technical burden associated with web deployment, MetaLIMS options the use of commercial web hosting combined with MetaLIMS bash scripts for ease of setup. MetaLIMS overcomes key challenges common in LIMS by giving labs access to a low-cost and open-source tool that also has the flexibility to meet individual lab needs and an option for easy deployment. By making the web application open source and hosting it on GitHub, we hope to encourage the community to build upon MetaLIMS, making it more robust and tailored to the needs of more researchers.
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Redrup MJ, Igarashi H, Schaefgen J, Lin J, Geisler L, Ben M'Barek M, Ramachandran S, Cardoso T, Hillewaert V. Sample Management: Recommendation for Best Practices and Harmonization from the Global Bioanalysis Consortium Harmonization Team. AAPS J 2016; 18:290-3. [PMID: 26821803 DOI: 10.1208/s12248-016-9869-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/07/2016] [Indexed: 11/30/2022]
Abstract
The importance of appropriate sample management in regulated bioanalysis is undeniable for clinical and non-clinical study support due to the fact that if the samples are compromised at any stage prior to analysis, the study results may be affected. Health authority regulations do not contain specific guidance on sample management; therefore, as part of the Global Bioanalysis Consortium (GBC), the A5 team was established to discuss sample management requirements and to put forward recommendations. The recommendations from the team concern the entire life span of the sample and include the following: 1. Sampling procedures should be described in the protocol or within the laboratory manual. This information should include the volume of the sample to be collected, the required anticoagulant, light sensitivity, collection and storage containers, and labeling with a unique identifier. 2. The correct procedures for processing and then storing the samples after collection at the clinical/non-clinical testing site and during shipment are also very important to ensure the analyte(s) stability and should be documented. 3. Chain of custody for the samples must be maintained throughout the complete life span of each sample. This is typically maintained via paper and electronic data systems, including Laboratory Information Management Systems (LIMS) where available. 4. Pre- and post-analysis storage location and conditions must also be clearly defined at the analytical laboratory. The storage temperature of the samples must be traceable and controlled by monitoring and warning alerts. The team suggests moving away from using temperatures and to adopt standard terminology of "room temperature," "refrigerator," "freezer," and "ultra-freezer" that have defined and industry-wide accepted temperature ranges. 5. At the end of the study, documentation of the samples' disposal is required.
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Affiliation(s)
- Michael J Redrup
- Quotient Bio Analytical Sciences (an LGC company), Newmarket, UK
| | | | | | - Jenny Lin
- CMIC, Inc, 2860 Forbs Avenue, Hoffman Estates, Illinois, 60192, USA.
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Abstract
Screening compounds precipitate out of high-concentration DMSO solutions and cause issues in the liquid-handling equipment used to process the samples as well as false-positives and false-negatives in the biological data. This report examines the extent of the precipitation issue, correlation with physico-chemical properties of compounds, and measured concentrations. Possible ways to allow recovery of the precipitated solids are also described. This study also investigated whether particulates were present from the time of initial solubilization in DMSO or whether precipitation occurs during freeze-thaw cycling.
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Affiliation(s)
- Ioana Popa-Burke
- Sample Management Technologies, Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, NC, USA
| | - John Russell
- Sample Management Technologies, Molecular Discovery Research, GlaxoSmithKline, Research Triangle Park, NC, USA
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