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However, to rely on these assays it is very important that quality is assured for all tests through a well-designed quality management system (QMS) which includes tools to register and verify the information regarding the tests. For research laboratories two important QMSs are the management systems from the [[International Organization for Standardization]] (ISO) and good laboratory practices (GLP). Good laboratory practices are defined by the Organization for Economic Cooperation and Development (OECD) as "a quality system concerned with the organizational process and the conditions under which non-clinical health and environmental safety studies are planned, performed, monitored, recorded, archived and reported."<ref name="OECDGuidance10">{{cite web |url=http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=env/jm/mono(2010)20&doclanguage=en |format=PDF |title=Guidance Document on Using Cytotoxicity Tests to Estimate Starting Doses for Acute Oral Systemic Toxicity Tests |author=Organisation for Economic Co-operation and Development |date=20 July 2010 |pages=54}}</ref><ref name="dosSantosBoas10">{{cite journal |title=Boas Práticas de Laboratório (BPL): Uma questão de qualidade |journal=Revista Intertox de Toxicologia, Risco Ambiental e Sociedade |author=dos Santos, P.E. |volume=3 |issue=2 |year=2010 |url=http://www.revistarevinter.com.br/minhas-revistas/2010/v-3-n-2-2010-volume-3-numero-2-junho-de-2010-sao-paulo/80-boas-praticas-de-laboratorio-bpl-uma-questao-de-qualidade/file |format=PDF}}</ref> The purpose of the GLP principles is to promote the development of quality test data and provide a tool to ensure a sound approach to the management of laboratory studies, including conduct, reporting and archiving. The GLP principles may be considered as a set of standards for ensuring the quality, reliability and integrity of studies, the reporting of verifiable conclusions and the traceability of data. The ISO management systems provide a model to follow when setting up and operating a laboratory according to a set of internationally recognized standards. They are the result of international expert consensus and therefore offer the benefit of global management experience and good practice.<ref name="ISOManagement">{{cite web |url=https://www.iso.org/management-system-standards.html |title=Management system standards |publisher=International Organization for Standardization}}</ref>
However, to rely on these assays it is very important that quality is assured for all tests through a well-designed quality management system (QMS) which includes tools to register and verify the information regarding the tests. For research laboratories two important QMSs are the management systems from the [[International Organization for Standardization]] (ISO) and good laboratory practices (GLP). Good laboratory practices are defined by the Organization for Economic Cooperation and Development (OECD) as "a quality system concerned with the organizational process and the conditions under which non-clinical health and environmental safety studies are planned, performed, monitored, recorded, archived and reported."<ref name="OECDGuidance10">{{cite web |url=http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=env/jm/mono(2010)20&doclanguage=en |format=PDF |title=Guidance Document on Using Cytotoxicity Tests to Estimate Starting Doses for Acute Oral Systemic Toxicity Tests |author=Organisation for Economic Co-operation and Development |date=20 July 2010 |pages=54}}</ref><ref name="dosSantosBoas10">{{cite journal |title=Boas Práticas de Laboratório (BPL): Uma questão de qualidade |journal=Revista Intertox de Toxicologia, Risco Ambiental e Sociedade |author=dos Santos, P.E. |volume=3 |issue=2 |year=2010 |url=http://www.revistarevinter.com.br/minhas-revistas/2010/v-3-n-2-2010-volume-3-numero-2-junho-de-2010-sao-paulo/80-boas-praticas-de-laboratorio-bpl-uma-questao-de-qualidade/file |format=PDF}}</ref> The purpose of the GLP principles is to promote the development of quality test data and provide a tool to ensure a sound approach to the management of laboratory studies, including conduct, reporting and archiving. The GLP principles may be considered as a set of standards for ensuring the quality, reliability and integrity of studies, the reporting of verifiable conclusions and the traceability of data. The ISO management systems provide a model to follow when setting up and operating a laboratory according to a set of internationally recognized standards. They are the result of international expert consensus and therefore offer the benefit of global management experience and good practice.<ref name="ISOManagement">{{cite web |url=https://www.iso.org/management-system-standards.html |title=Management system standards |publisher=International Organization for Standardization}}</ref>
The recognition of compliance to quality management principles by laboratories can be complex. This process can be slow and costly, potentially requiring changes in laboratory routine. Recognition and maintenance of compliance to these principles is also difficult because it requires that the laboratory maintains a continuing routine of activities that include training of staff, maintenance of facilities and equipment, monitoring document and lab record quality, inspection of calendars and periodic reporting. Manual capture, calculation and verification of raw data result in a tremendous drain on human resources while also jeopardizing the integrity of the information. The administration of paper records is particularly inefficient and expensive, and data cannot be easily integrated with other technologies. As a result, complying with the strict principles of quality systems can be a very time consuming and expensive process. Thus, the use of computer systems capable of addressing the complexity of the regulations, ensuring compliance with current best practice and satisfying the concerns and expectations of the regulators is pressing. The main tool that can assist in this process is the [[laboratory information management system]] (LIMS), which allows the recording of lab activities in a complete and easy way. All data are recorded in databases and the relationship between the experimental steps is logged, allowing the traceability of samples and the documentation of chain of custody, reagents and results.<ref name="HintonLab94">{{cite book |title=Laboratory Information Management Systems: Development and Implementation for a Quality Assurance Laboratory |author=Hinton, M.D. |publisher=Marcel Dekker, Inc |year=1994 |isbn=0824794583}}</ref><ref name="PaszkoLab01">{{cite book |title=Laboratory Information Management Systems |author=Paszko, C.; Turner, E. |publisher=CRC Press |year=2001 |pages=242 |isbn=9780824705213}}</ref> An extensive list of LIMS can be found nowadays, and several LIMS are currently available as academic, proprietary and open-source solutions. Some examples of these include [[LabLite, LLC|SQL LIMS]]<ref name="LabLite">{{cite web |url=http://www.lablite.com/ |title=LabLite |publisher=LabLite, LLC}}</ref>, [[Computing Solutions, Inc.|LabSoft]]<ref name="CSI">{{cite web |url=http://www.labsoftlims.com/ |title=LabSoft LIMS |publisher=Computing Solutions, Inc}}</ref>, [[LabWare, Inc.|LabWare]]<ref name="LabWare">{{cite web |url=http://www.labware.com/en |title=LabWare |publisher=LabWare, Inc}}</ref>, [[LIMS at work GmbH#History|FreeLIMS]]<ref name="FreeLIMS">{{cite web |url=https://sourceforge.net/projects/freelims/ |title=FreeLIMS |work=SourceForge |publisher=Slashdot Media}}</ref>, [[Ocimum Biosolutions Ltd.|Biotracker]]<ref name="Biotracker">{{cite web |url=https://www.ocimumbio.com/biotrackertm/ |title=Biotracker LIMS |publisher=Ocimum Biosolutions Ltd}}</ref>, [[Thermo Scientific|Watson]]<ref name="Watson">{{cite web |url=https://www.thermofisher.com/order/catalog/product/INF-21000 |title=Watson LIMS Software |publisher=Thermo Fisher Scientific}}</ref> and the systems developed by Hendricks<ref name="HendricksALab03">{{cite journal |title=A laboratory information management system (LIMS) for an academic microchip fabrication facility |journal=Proceedings of the 15th Biennial University/Government/Industry Microelectronics Symposium, 2003 |author=Hendricks, R.W.; Learn, M.R. |year=2003 |doi=10.1109/UGIM.2003.1225703}}</ref>, Quo<ref name="QuoDevelopment05">{{cite journal |title=Development of a laboratory information system for cancer collaboration projects |journal=Conference Proceedings from the Annual International Conference of the IEEE Engineering in Medicine and Biology Society |author=Quo, C.F.; Wu, B.; Wang, M.D. |volume=3 |pages=2859-62 |year=2005 |doi=10.1109/IEMBS.2005.1617070 |pmid=17282839}}</ref>, Tharayil<ref name="Tharayil">{{cite journal |title=Service-Oriented Laboratory Information Management System for Life Sciences Research |journal=IEEE International Conference on Services Computing, 2007 |author=Tharayil, S.M.; Kalbfleisch, T.; Kumar, A. |year=2007 |doi=10.1109/SCC.2007.103}}</ref> and Sanchez-Villeda.<ref name="Sanchez-VilledaDevelop03">{{cite journal |title=Development of an integrated laboratory information management system for the maize mapping project |journal=Bioinformatics |author=Sanchez-Villeda, H.; Schroeder, S.; Polacco, M. et al. |volume=19 |issue=16 |pages=2022-30 |year=2003 |pmid=14594706}}</ref>


==References==
==References==
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==Notes==
==Notes==
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. Some grammar were corrected when necessary.
This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. Some grammar were corrected when necessary. Several of the original URLs have changed since 2015 and have been updated to current here.


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Revision as of 22:20, 31 July 2017

Full article title FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data
Journal BMC Bioinformatics
Author(s) Faria-Campos, Alessandra C.; Balottin, Luciene B.; Zuin, Gianlucca; Garcia, Vinicius;
Batista, Paulo H.S.; Granjeiro, José M.; Campos, Sérgio V.A.
Author affiliation(s) Universidade Federal de Minas Gerais, INMETRO
Primary contact Email: alessa at dcc dot ufmg dot br
Year published 2015
Volume and issue 16(Suppl 19)
Page(s) 58
DOI 10.1186/1471-2105-16-S19-S8
ISSN 1471-2105
Distribution license Creative Commons Attribution 4.0 International
Website https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-16-S19-S8
Download https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-16-S19-S8 (PDF)
This article should not be considered complete until this message box has been removed. This is a work in progress.

Abstract

Background: Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical. These assays may be used as an alternative to animal experimentation and are becoming increasingly important in modern laboratories. However, the execution of these assays in large-scale and different laboratories requires, among other things, the management of protocols, reagents, and cell lines used, as well as the data produced, which can be a challenge. The management of all this information is greatly improved by the utilization of computational tools to save time and guarantee quality. However, a tool that performs this task designed specifically for cytotoxicity assays is not yet available.

Results: In this work, we have used a workflow based LIMS — the Flux system — and the Together Workflow Editor as a framework to develop FluxCTTX, a tool for management of data from cytotoxicity assays performed at different laboratories. The main work is the development of a workflow, which represents all stages of the assay and has been developed and uploaded in Flux. This workflow models the activities of cytotoxicity assays performed as described in the OECD 129 Guidance Document.

Conclusions: FluxCTTX presents a solution for the management of the data produced by cytotoxicity assays performed at interlaboratory comparisons. Its adoption will contribute to guarantee the quality of activities in the process of cytotoxicity tests and enforce the use of good laboratory practices (GLP). Furthermore, the workflow developed is complete and can be adapted to other contexts and different tests for management of other types of data.

Keywords: laboratory information management systems, workflow, cytotoxicity tests, OECD129, Good Laboratory Practices, interlaboratory comparison

Background

Cytotoxicity is the quality of being toxic to cells. Examples of toxic agents are some types of venom (e.g., from the puff adder or brown recluse spider). Treating cells with the cytotoxic compound can result in a variety of cell fates: The cells may undergo necrosis, stop actively growing and dividing or activate a genetic program of controlled cell death (apoptosis). Cytotoxicity assays are the tests used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds, if they are interested in developing a therapeutic that targets rapidly dividing cells, or they can screen "hits" from initial high-throughput drug screens for unwanted cytotoxic effects before investing in their development as a pharmaceutical.

Cytotoxicity tests may be used as a substitute to in vivo tests that use animals. The concept of using in vitro cytotoxicity data to determine the starting doses for rodent acute oral toxicity tests was discussed and evaluated at the International Workshop on In Vitro Methods for Assessing Acute Systemic Toxicity convened in 2000.[1] The approach involves using an IC50 value from an in vitro basal cytotoxicity test with the Registry of Cytotoxicity (RC) regression to predict an LD50 value for use as a starting dose for the Acute Toxic Class (ATC) method or the Up-and-Down Procedure (UDP) test method.[2] Simulations showed that using in vitro cytotoxicity assays to estimate an LD50 to use as a starting dose in the UDP could potentially reduce animal use by 25 to 40 percent. Additionally, several tests have currently demonstrated the efficiency and effectiveness of alternative methods testing to reduce, refine, and/or replace the use of animals in testing.[1][2][3][4][5]

However, to rely on these assays it is very important that quality is assured for all tests through a well-designed quality management system (QMS) which includes tools to register and verify the information regarding the tests. For research laboratories two important QMSs are the management systems from the International Organization for Standardization (ISO) and good laboratory practices (GLP). Good laboratory practices are defined by the Organization for Economic Cooperation and Development (OECD) as "a quality system concerned with the organizational process and the conditions under which non-clinical health and environmental safety studies are planned, performed, monitored, recorded, archived and reported."[6][7] The purpose of the GLP principles is to promote the development of quality test data and provide a tool to ensure a sound approach to the management of laboratory studies, including conduct, reporting and archiving. The GLP principles may be considered as a set of standards for ensuring the quality, reliability and integrity of studies, the reporting of verifiable conclusions and the traceability of data. The ISO management systems provide a model to follow when setting up and operating a laboratory according to a set of internationally recognized standards. They are the result of international expert consensus and therefore offer the benefit of global management experience and good practice.[8]

The recognition of compliance to quality management principles by laboratories can be complex. This process can be slow and costly, potentially requiring changes in laboratory routine. Recognition and maintenance of compliance to these principles is also difficult because it requires that the laboratory maintains a continuing routine of activities that include training of staff, maintenance of facilities and equipment, monitoring document and lab record quality, inspection of calendars and periodic reporting. Manual capture, calculation and verification of raw data result in a tremendous drain on human resources while also jeopardizing the integrity of the information. The administration of paper records is particularly inefficient and expensive, and data cannot be easily integrated with other technologies. As a result, complying with the strict principles of quality systems can be a very time consuming and expensive process. Thus, the use of computer systems capable of addressing the complexity of the regulations, ensuring compliance with current best practice and satisfying the concerns and expectations of the regulators is pressing. The main tool that can assist in this process is the laboratory information management system (LIMS), which allows the recording of lab activities in a complete and easy way. All data are recorded in databases and the relationship between the experimental steps is logged, allowing the traceability of samples and the documentation of chain of custody, reagents and results.[9][10] An extensive list of LIMS can be found nowadays, and several LIMS are currently available as academic, proprietary and open-source solutions. Some examples of these include SQL LIMS[11], LabSoft[12], LabWare[13], FreeLIMS[14], Biotracker[15], Watson[16] and the systems developed by Hendricks[17], Quo[18], Tharayil[19] and Sanchez-Villeda.[20]

References

  1. ↑ 1.0 1.1 Interagency Coordinating Committee on the Validation of Alternative Methods (August 2001). "Report of the International Workshop on In Vitro Methods for Assessing Acute Systemic Toxicity" (PDF). National Institute of Environmental Health Sciences. https://ntp.niehs.nih.gov/iccvam/docs/acutetox_docs/finalrpt/finalall0801.pdf. 
  2. ↑ 2.0 2.1 Spielmann, H.; Genschow, E.; Liebsch, M.; Halle, W. (1999). "Determination of the Starting Dose for Acute Oral Toxicity (LD50) Testing in the Up and Down Procedure (UDP) From Cytotoxicity Data". Alternatives to Laboratory Animals 27 (6): 957-66. PMID 25490464. 
  3. ↑ Stokes, W.S.; Casati, S.; Strickland, J.; Paris, M. (2008). "Neutral red uptake cytotoxicity tests for estimating starting doses for acute oral toxicity tests". Current Protocols in Toxicology 36 (20.4): 20.4.1–20.4.20. doi:10.1002/0471140856.tx2004s36. PMID 20967741. 
  4. ↑ EURL ECVAM (December 2014). "EURL ECVAM strategy to replace, reduce and refine the use of animals in the assessment of acute mammalian systemic toxicity". European Commission. pp. 46. https://eurl-ecvam.jrc.ec.europa.eu/eurl-ecvam-strategy-papers/strategy-acute-mammalian-systemic-toxicity. 
  5. ↑ National Institute of Environmental Health Sciences. "Alternatives to Animal Testing". National Institutes of Health. https://www.niehs.nih.gov/health/topics/science/sya-iccvam/. 
  6. ↑ Organisation for Economic Co-operation and Development (20 July 2010). "Guidance Document on Using Cytotoxicity Tests to Estimate Starting Doses for Acute Oral Systemic Toxicity Tests" (PDF). pp. 54. http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=env/jm/mono(2010)20&doclanguage=en. 
  7. ↑ dos Santos, P.E. (2010). "Boas Práticas de Laboratório (BPL): Uma questão de qualidade" (PDF). Revista Intertox de Toxicologia, Risco Ambiental e Sociedade 3 (2). http://www.revistarevinter.com.br/minhas-revistas/2010/v-3-n-2-2010-volume-3-numero-2-junho-de-2010-sao-paulo/80-boas-praticas-de-laboratorio-bpl-uma-questao-de-qualidade/file. 
  8. ↑ "Management system standards". International Organization for Standardization. https://www.iso.org/management-system-standards.html. 
  9. ↑ Hinton, M.D. (1994). Laboratory Information Management Systems: Development and Implementation for a Quality Assurance Laboratory. Marcel Dekker, Inc. ISBN 0824794583. 
  10. ↑ Paszko, C.; Turner, E. (2001). Laboratory Information Management Systems. CRC Press. pp. 242. ISBN 9780824705213. 
  11. ↑ "LabLite". LabLite, LLC. http://www.lablite.com/. 
  12. ↑ "LabSoft LIMS". Computing Solutions, Inc. http://www.labsoftlims.com/. 
  13. ↑ "LabWare". LabWare, Inc. http://www.labware.com/en. 
  14. ↑ "FreeLIMS". SourceForge. Slashdot Media. https://sourceforge.net/projects/freelims/. 
  15. ↑ "Biotracker LIMS". Ocimum Biosolutions Ltd. https://www.ocimumbio.com/biotrackertm/. 
  16. ↑ "Watson LIMS Software". Thermo Fisher Scientific. https://www.thermofisher.com/order/catalog/product/INF-21000. 
  17. ↑ Hendricks, R.W.; Learn, M.R. (2003). "A laboratory information management system (LIMS) for an academic microchip fabrication facility". Proceedings of the 15th Biennial University/Government/Industry Microelectronics Symposium, 2003. doi:10.1109/UGIM.2003.1225703. 
  18. ↑ Quo, C.F.; Wu, B.; Wang, M.D. (2005). "Development of a laboratory information system for cancer collaboration projects". Conference Proceedings from the Annual International Conference of the IEEE Engineering in Medicine and Biology Society 3: 2859-62. doi:10.1109/IEMBS.2005.1617070. PMID 17282839. 
  19. ↑ Tharayil, S.M.; Kalbfleisch, T.; Kumar, A. (2007). "Service-Oriented Laboratory Information Management System for Life Sciences Research". IEEE International Conference on Services Computing, 2007. doi:10.1109/SCC.2007.103. 
  20. ↑ Sanchez-Villeda, H.; Schroeder, S.; Polacco, M. et al. (2003). "Development of an integrated laboratory information management system for the maize mapping project". Bioinformatics 19 (16): 2022-30. PMID 14594706. 

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. Some grammar were corrected when necessary. Several of the original URLs have changed since 2015 and have been updated to current here.

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