1
|
Timóteo M, Lourenço E, Brochado AC, Domenico L, da Silva J, Oliveira B, Barbosa R, Montemezzi P, Mourão CFDAB, Olej B, Alves G. Digital Management Systems in Academic Health Sciences Laboratories: A Scoping Review. Healthcare (Basel) 2021; 9:healthcare9060739. [PMID: 34208584 PMCID: PMC8234580 DOI: 10.3390/healthcare9060739] [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: 05/15/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 01/02/2023] Open
Abstract
Good laboratory practices (GLP) increase the quality and traceability of results in health sciences research. However, factors such as high staff turnover, insufficient resources, and a lack of training for managers may limit their implementation in research and academic laboratories. This Scoping Review aimed to identify digital tools for managing academic health sciences and experimental medicine laboratories and their relationship with good practices. Following the PRISMA-ScR 2018 criteria, a search strategy was conducted until April 2021 in the databases PUBMED, Web of Sciences, and Health Virtual Library. A critical appraisal of the selected references was conducted, followed by data charting. The search identified twenty-one eligible articles, mainly originated from high-income countries, describing the development and/or implementation of thirty-two electronic management systems. Most studies described software functionalities, while nine evaluated and discussed impacts on management, reporting both improvements in the workflow and system limitations during implementation. In general, the studies point to a contribution to different management issues related to GLP principles. In conclusion, this review identified evolving evidence that digital laboratory management systems may represent important tools in compliance with the principles of good practices in experimental medicine and health sciences research.
Collapse
Affiliation(s)
- Margareth Timóteo
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
- Post-Graduation Program in Medical Sciences, Fluminense Federal University, Niteroi 24020-140, Brazil
| | - Emanuelle Lourenço
- Post-Graduation Program in Dentistry, Fluminense Federal University, Niteroi 24020-140, Brazil;
| | - Ana Carolina Brochado
- Post-Graduation Program in Science and Biotechnology, Fluminense Federal University, Niteroi 24020-140, Brazil; (A.C.B.); (R.B.)
| | - Luciana Domenico
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
| | - Joice da Silva
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
| | - Bruna Oliveira
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
| | - Renata Barbosa
- Post-Graduation Program in Science and Biotechnology, Fluminense Federal University, Niteroi 24020-140, Brazil; (A.C.B.); (R.B.)
| | | | - Carlos Fernando de Almeida Barros Mourão
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
- Post-Graduation Program in Science and Biotechnology, Fluminense Federal University, Niteroi 24020-140, Brazil; (A.C.B.); (R.B.)
- Correspondence: (C.F.d.A.B.M.); (G.A.); Tel.: +1-941-830-1302 (C.F.d.A.B.M.); +55-21-26299255 (G.A.)
| | - Beni Olej
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
| | - Gutemberg Alves
- Clinical Research Unit, Antônio Pedro Hospital, Fluminense Federal University, Niteroi 24020-140, Brazil; (M.T.); (L.D.); (J.d.S.); (B.O.); (B.O.)
- Correspondence: (C.F.d.A.B.M.); (G.A.); Tel.: +1-941-830-1302 (C.F.d.A.B.M.); +55-21-26299255 (G.A.)
| |
Collapse
|
2
|
Carvajal C, Vallejos C, Lemaitre D, Ruiz J, Guzmán C, Aguilera V, Baño D, Calligaris SD. A REDCap application that links researchers, animal facility staff and members of the IACUC in animal health monitoring. Lab Anim 2018; 53:500-507. [PMID: 30526294 DOI: 10.1177/0023677218815723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research studies involving animal experimentation are regulated by the Institutional Animal Care and Use Committee (IACUC). To this end, the IACUC must integrate the information provided by the investigators of each preclinical study and the veterinarians from the animal facility in order to monitor and approve the process. Using a paper-based system to collect animal health and welfare data is a common, albeit time-consuming practice, prone to transcription and reading errors, not to mention inconvenient for veterinarians and investigators wishing to make timely and collaborative decisions when animal welfare is at risk. We created a web-based monitoring system focused on animal health with the potential to improve animal welfare. The data management system is based on REDCap software, which enables data integration in order to offer a solution for animal welfare assessment. The proposed scheme includes key indicators of general health status, such as environment, physical/nutritional information, and behavioral parameters during animal breeding and experimentation, as important components of animal welfare. In addition, the system facilitates communication of this information among researchers, animal facility staff, and the IACUC. REDCap is available to non-profit organizations, and may be adapted and replicated by institutions interested in and responsible for animal care, and used in research. REDCap is an excellent tool for promoting good practices that benefit experimental animal health.
Collapse
Affiliation(s)
- Cristobal Carvajal
- Instituto de Ciencias e Innovación en Medicina, Clínica Alemana Facultad de Medicina, Clinica Alemana, Universidad del Desarrollo, Chile
| | - Catalina Vallejos
- Laboratory Animal Facility, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile
| | - Dominique Lemaitre
- Centro de Fisiología Celular e Integrativa, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Jorge Ruiz
- Laboratory Animal Facility, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile
| | - Camila Guzmán
- Tecnología Médica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile
| | - Valentina Aguilera
- Tecnología Médica, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile
| | - Diego Baño
- Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Chile
| | - Sebastián D Calligaris
- Centro de Medicina Regenerativa Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Chile
| |
Collapse
|
3
|
Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V. Principles and application of LIMS in mouse clinics. Mamm Genome 2015. [PMID: 26208973 PMCID: PMC4602070 DOI: 10.1007/s00335-015-9586-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen & paper colony management, spreadsheet-based data management and manual data analysis. Hence, different Laboratory Information Management Systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.
Collapse
Affiliation(s)
- Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ralph Steinkamp
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anja Hurt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Elida Schneltzer
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Philipp Gormanns
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Christoph Lengger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Melvin
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Neha Agrawal
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Rafael Alcantara
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Arthur Evans
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Gannon
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Simon Holroyd
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Christian Kipp
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Navis Pretheeba Raj
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Richardson
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Sophie LeBlanc
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Laurent Vasseur
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Hiroshi Masuya
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Kimio Kobayashi
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Tomohiro Suzuki
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Nobuhiko Tanaka
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Shigeharu Wakana
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Alison Walling
- Mary Lyon Centre, Medical Research Council Harwell, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
| | - David Clary
- Mouse Biology Program, University of California, Davis, 2795 2nd Street, Suite 400, Davis, CA, 95618, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Chair for Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität Munich, Freising-Weihenstephan, 85354, Munich, Germany. .,Member of German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| |
Collapse
|
4
|
O’Farrell B, Haase JK, Velayudhan V, Murphy RA, Achtman M. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains. PLoS One 2012; 7:e48022. [PMID: 23144721 PMCID: PMC3483277 DOI: 10.1371/journal.pone.0048022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 09/20/2012] [Indexed: 11/30/2022] Open
Abstract
Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST) of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS) consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of < €25 per strain. Since developing this pipeline, >200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.
Collapse
Affiliation(s)
- Brian O’Farrell
- Environmental Research Institute, University College Cork, Cork, Ireland
- * E-mail: (MA); (JKH); (BOF)
| | - Jana K. Haase
- Environmental Research Institute, University College Cork, Cork, Ireland
- * E-mail: (MA); (JKH); (BOF)
| | | | - Ronan A. Murphy
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Mark Achtman
- Environmental Research Institute, University College Cork, Cork, Ireland
- * E-mail: (MA); (JKH); (BOF)
| |
Collapse
|
6
|
Russom D, Ahmed A, Gonzalez N, Alvarnas J, DiGiusto D. Implementation of a configurable laboratory information management system for use in cellular process development and manufacturing. Cytotherapy 2011; 14:114-21. [PMID: 21973024 DOI: 10.3109/14653249.2011.619007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AIMS Regulatory requirements for the manufacturing of cell products for clinical investigation require a significant level of record-keeping, starting early in process development and continuing through to the execution and requisite follow-up of patients on clinical trials. Central to record-keeping is the management of documentation related to patients, raw materials, processes, assays and facilities. METHODS To support these requirements, we evaluated several laboratory information management systems (LIMS), including their cost, flexibility, regulatory compliance, ongoing programming requirements and ability to integrate with laboratory equipment. After selecting a system, we performed a pilot study to develop a user-configurable LIMS for our laboratory in support of our pre-clinical and clinical cell-production activities. We report here on the design and utilization of this system to manage accrual with a healthy blood-donor protocol, as well as manufacturing operations for the production of a master cell bank and several patient-specific stem cell products. RESULTS The system was used successfully to manage blood donor eligibility, recruiting, appointments, billing and serology, and to provide annual accrual reports. Quality management reporting features of the system were used to capture, report and investigate process and equipment deviations that occurred during the production of a master cell bank and patient products. CONCLUSIONS Overall the system has served to support the compliance requirements of process development and phase I/II clinical trial activities for our laboratory and can be easily modified to meet the needs of similar laboratories.
Collapse
Affiliation(s)
- Diana Russom
- Department of Information Technology Systems, City of Hope, Duarte, California 91010, USA
| | | | | | | | | |
Collapse
|