|
|
| (99 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| '''PCR considerations'''
| | {{Saved book |
| | |title=Introduction to Quality and Quality Management Systems |
| | |subtitle= |
| | |cover-image=Time-Quality-Money.png |
| | |cover-color=#fffccc |
| | | setting-papersize = A4 |
| | | setting-showtoc = 1 |
| | | setting-columns = 1 |
| | }} |
|
| |
|
| Whether adding PCR to your existing laboratory, modifying existing PCR workflows, or starting from scratch, preventing contamination is a top priority. As PCR can effectively amplify even the tiniest of quantities of DNA and RNA, the risk of amplifying a contaminant and ruining the validity of an assay is very real.<ref name="MifflinSetting03">{{cite book |url=http://www.biosupplynet.com/pdf/01_pcr_primer_p.5_14.pdf |format=PDF |chapter=Chapter 1: Setting Up a PCR Laboratory |title=PCR Primer |author=Mifflin, T.E. |editor=Dieffenbach, C.; Dveksler, G. |edition=2nd |publisher=Cold Spring Harbor Laboratory Press |pages=5–14 |year=2003 |isbn=9780879696542 |accessdate=13 August 2020}}</ref><ref name="RochePCR06">{{cite book |url=https://www.gene-quantification.de/ras-pcr-application-manual-3rd-ed.pdf |format=PDF |chapter=Chapter 2: General Guidelines |title=PCR Applications Manual |editor=Degen, H.-J.; Deufel, A.; Eisel, D. et al. |edition=3rd |publisher=Roche Diagnostics GmbH |pages=19–38 |year=2006 |accessdate=13 August 2020}}</ref><ref name="AhmedSetting14">{{cite book |url=http://grcpk.com/wp-content/uploads/2014/10/12.-Setting-up-PCR-Lab.pdf |format=PDF |chapter=Chapter 12: Setting-up a PCR Lab |title=Manual of PCR |author=Ahmed, S. |publisher=Genetics Resource Centre |year=2014 |accessdate=13 August 2020}}</ref><ref name="RedigTheDevil14">{{cite web |url=https://bitesizebio.com/19880/the-devil-is-in-the-details-how-to-setup-a-pcr-laboratory/ |title=The Devil is in the Details: How to Setup a PCR Laboratory |author=Redig, J. |work=BiteSizeBio |date=01 August 2014 |accessdate=13 August 2020}}</ref><ref name="BioChekTheBasics18">{{cite web |url=https://www.biochek.com/wp-content/uploads/2018/05/BioChek-E-book-The-basics-of-PCR.pdf |format=PDF |title=The basics of PCR: Detecting viruses and bacteria red-handed |publisher=BioChek BV |date=May 2018 |accessdate=13 August 2020}}</ref><ref name="DasMitig18">{{cite journal |title=Mitigating PCR /Amplicon Contamination in a High Risk High Burden Mycobacterial Reference Laboratory in a Resource Limited Setting |journal=Mycobacterial Diseases |author=Das, P.K.; Ganguly, S.B.; Mandal, B. |volume=8 |issue=2 |at=261 |year=2018 |doi=10.4172/2161-1068.1000261}}</ref><ref name="WHODos18">{{cite web |url=https://www.who.int/teams/global-malaria-programme/case-management/diagnosis/nucleic-acid-amplification-based-diagnostics/dos-and-don-ts-for-molecular-testing |title=Dos and Don'ts for molecular testing |author=World Health Organization |publisher=World Health Organization |date=31 January 2018 |accessdate=08 September 2021}}</ref> Contamination typically comes from non-amplified environmental substances such as aerosols, and from carryover contamination of amplicons from earlier PCR cycles. As such, not only do best-practice processes and procedures (P&P) need to be followed (e.g., unidirectional workflow, thorough cleaning procedures, proper preparation and disposal), but also where to place PCR-related equipment must be carefully considered.<ref name="MifflinSetting03" /><ref name="RochePCR06" /><ref name="RedigTheDevil14" /><ref name="DasMitig18" />
| | ==''Introduction to Quality and Quality Management Systems''== |
| | {{ombox |
| | | type = content |
| | | style = width: 500px; |
| | | text = This book should not be considered complete until this message box has been removed. This is a work in progress. |
| | }} |
| | The goal of this short volume is to act as an introduction to the quality management system. It collects several articles related to quality, quality management, and associated systems. |
|
| |
|
| When possible, separate rooms for sample preparation, PCR setup, and post-PCR activities, each with their own airflow control, are encouraged.<ref name="MifflinSetting03" /><ref name="RochePCR06" /><ref name="BioChekTheBasics18" /><ref name="DasMitig18" /><ref name="WHODos18" /> However, the laboratory attempting to add PCR to an already small clinical diagnostic lab may not have the luxury of having multiple rooms. In that case, a single-room setup may suffice, if the workflow areas remain demarcated or physically partitioned. Additionally, a single-room setup must also have stricter P&P and design controls to offset the space constraints. For example, the sample preparation area of the room should have a laminar flow hood with UV light that is regularly cleaned, and post-PCR analysis may need to occur later in the day after cleanup from prior steps.<ref name="MifflinSetting03" /><ref name="AhmedSetting14" /><ref name="WHODos18" /> Of course, always maintaining unidirectional workflow—regardless of number of rooms—is also critical to minimizing contamination. For example, technicians shouldn't be transporting amplified materials into the DNA extraction area.
| | ;1. What is quality? |
| | :''Key terms'' |
| | :[[Quality (business)|Quality]] |
| | :[[Quality assurance]] |
| | :[[Quality control]] |
| | :''The rest'' |
| | :[[Data quality]] |
| | :[[Information quality]] |
| | :[[Nonconformity (quality)|Nonconformity]] |
| | :[[Service quality]] |
| | ;2. Processes and improvement |
| | :[[Business process]] |
| | :[[Process capability]] |
| | :[[Risk management]] |
| | :[[Workflow]] |
| | ;3. Mechanisms for quality |
| | :[[Acceptance testing]] |
| | :[[Conformance testing]] |
| | :[[Clinical quality management system]] |
| | :[[Continual improvement process]] |
| | :[[Corrective and preventive action]] |
| | :[[Good manufacturing practice]] |
| | :[[Malcolm Baldrige National Quality Improvement Act of 1987]] |
| | :[[Quality management]] |
| | :[[Quality management system]] |
| | :[[Total quality management]] |
| | ;4. Quality standards |
| | :[[ISO 9000]] |
| | :[[ISO 13485]] |
| | :[[ISO 14000|ISO 14001]] |
| | :[[ISO 15189]] |
| | :[[ISO/IEC 17025]] |
| | :[[ISO/TS 16949]] |
| | ;5. Quality in software |
| | :[[Software quality]] |
| | :[[Software quality assurance]] |
| | :[[Software quality management]] |
|
| |
|
| Although dated, Roche Diagnostics' 2006 ''[https://www.gene-quantification.de/ras-pcr-application-manual-3rd-ed.pdf PCR Applications Manual]''<ref name="RochePCR06" /> provides a detailed breakdown of setting up the laboratory for PCR. [https://www.longdom.org/open-access/mitigating-pcr-amplicon-contamination-in-a-high-risk-high-burden-mycobacterial-reference-laboratory-in-a-resource-limited-setting-2161-1068-1000261.pdf Das ''et al.'']<ref name="DasMitig18" /> and [https://bitesizebio.com/19880/the-devil-is-in-the-details-how-to-setup-a-pcr-laboratory/ Dr. Jennifer Redig]<ref name="RedigTheDevil14" /> provide additional valuable insight. The World Health Organization (WHO) also provides [https://www.who.int/teams/global-malaria-programme/case-management/diagnosis/nucleic-acid-amplification-based-diagnostics/dos-and-don-ts-for-molecular-testing guidance] for setting up molecular testing in the lab.<ref name="WHODos18" />
| | <!--Place all category tags here--> |
| | |
| '''Isothermal amplification considerations'''
| |
| | |
| Similarly, because DNA and RNR amplification is involved, contamination concerns exist with isothermal amplification techniques. Multiple pipetting steps and repeated freezing and thawing of reagents can still lead to cross-contamination<ref name="DiegoProgress19">{{cite journal |title=Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: Towards a ready-to-use test |journal=Scientific Reports |author=Diego, J. G.-B.; Fernández-Soto, P.; Crego-Vicente, B. et al. |volume=9 |at=14744 |year=2019 |doi=10.1038/s41598-019-51342-2 |pmid=31611563 |pmc=PMC6791938}}</ref>, as does opening the reaction chamber after reaction is completed.<ref name="MartzyChall19">{{cite journal |title=Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis |journal=Analytical and Bioanalytical Chemistry |author=Martzy, R.; Kolm, C.; Krska, R. et al. |volume=411 |pages=1695–1702 |year=2019 |doi=10.1007/s00216-018-1553-1 |pmid=30617408 |pmc=PMC6453865}}</ref> However, the advent of microfluidics and lateral flow technologies in isothermal amplification processes has seen the development of "fully enclosed microstructured devices into which performing the isothermal amplification reduces the risk of sample contamination and allows integration and portable device realization."<ref name="ZanoliIsotherm13">{{cite journal |title=Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices |journal=Biosensors |author=Zanoli, L.M.; Spoto, G. |volume=3 |issue=1 |pages=18–43 |year=2013 |doi=10.3390/bios3010018 |pmid=25587397 |pmc=PMC4263587}}</ref><ref name="RoskosSimple13">{{cite journal |title=Simple System for Isothermal DNA Amplification Coupled to Lateral Flow Detection |journal=PLoS One |author=Roskos, K.; Hickerson, A.I.; Lu, H.-W. et al. |volume=8 |issue=7 |at=e69355 |year=2013 |doi=10.1371/journal.pone.0069355 |pmid=23922706 |pmc=PMC3724848}}</ref> Even more cutting-edge techniques to reduce contamination such as the CUT-LAMP technique of Bao ''et al.''<ref name="BaoCUT20">{{cite journal |title=CUT-LAMP: Contamination-Free Loop-Mediated Isothermal Amplification Based on the CRISPR/Cas9 Cleavage |journal=ACS Sensors |author=Bao, Y.; Jiang, Y.; Xiong, E. et al. |volume=5 |issue=4 |pages=1082–91 |year=2020 |doi=10.1021/acssensors.0c00034 |pmid=32242409}}</ref> or the dUTP/UDG system for COVID-19 RT-LAMP reactions of Kellner ''et al.''<ref name="KellnerARapid20">{{cite journal |title=A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing |journal=bioRxiv |author=Kellner, M.J.; Ross, J.J.; Schnabl, J. et al. |year=2020 |doi=10.1101/2020.06.23.166397}}</ref> hold further promise in making isothermal amplification processes in the laboratory easier to manage. That said, labs running isothermal amplification processes such as LAMP requiring analysis with agarose gel electrophoresis or a method requiring the opening of reaction vessels will preferably have a secondary area set up for analysis steps so as to minimize the chances of contamination.<ref name="NEBLoop14">{{cite web |url=https://www.neb.com/protocols/2014/06/17/loop-mediated-isothermal-amplification-lamp |title=Loop-mediated Isothermal Amplification (LAMP) |publisher=New England BioLabs |date=17 June 2014 |accessdate=14 August 2020}}</ref><ref name="Fernández-SotoDevelop14">{{cite journal |title=Development of a Highly Sensitive Loop-Mediated Isothermal Amplification (LAMP) Method for the Detection of ''Loa loa'' |journal=PLoS One |author=Fernández-Soto, P.; Mvoulouga, P.O.; Akue, J.P. et al. |volume=9 |issue=4 |at=e94664 |year=2014 |doi=10.1371/journal.pone.0094664 |pmid=24722638 |pmc=PMC3983228}}</ref>
| |
| | |
| ==References==
| |
| {{Reflist|colwidth=30em}}
| |
