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| Polymerase chain reaction or PCR is a molecular biology method that takes small amounts of DNA sequences and makes copies of (amplifies) them to the point of having enough material to sufficiently study or work with. The base technique can yield results in several hours and has a high level of sensitivity, with its ability to amplify the DNA to counts of millions or billions. PCR has been used in molecular diagnostics for testing prospective parents for being genetic carriers of particular diseases (i.e., expanded carrier screening)<ref name="GreggExpanded18">{{cite journal |title=Expanded Carrier Screening |journal=Obstetrics and Gynecology Clinics of North America |author=Gregg, A.R. |volume=45 |issue=1 |pages=103–112 |year=2018 |doi=10.1016/j.ogc.2017.10.005 |pmid=29428278}}</ref><ref name="ChokoschviliRepro18">{{cite journal |title=Reproductive autonomy in expanded carrier screening: More than meets the eye? |journal=Expert Review of Molecular Diagnostics |author=Chokoshvili, D.; Vears, D.F.; Borry, P. |volume=18 |issue=12 |pages=993–94 |year=2018 |doi=10.1080/14737159.2018.1544496 |pmid=30394810}}</ref>, tissue typing to ensure more effective organ transplants<ref name="EdgerlyThePast18">{{cite journal |title=The Past, Present, and Future of HLA Typing in Transplantation |journal=Methods in Molecular Biology |author=Edgerly, C.H.; Weimer, E.T. |volume=1802 |pages=1–10 |year=2018 |doi=10.1007/978-1-4939-8546-3_1 |pmid=29858798}}</ref>, and analyzing mutations in oncogenes to customize cancer treatments.<ref name="LodaPoly94">{{cite journal |title=Polymerase chain reaction-based methods for the detection of mutations in oncogenes and tumor suppressor genes |journal=Human Pathology |author=Loda, M. |volume=25 |issue=6 |pages=564–71 |year=1994 |doi=10.1016/0046-8177(94)90220-8 |pmid=7912220}}</ref> However, the method has also been applied to [[forensic science]]<ref name="NinfaFund09">{{Cite book |url=https://books.google.com/books?id=k6_XQwAACAAJ&pg=PA408 |title=Fundamental Laboratory Approaches for Biochemistry and Biotechnology |author=Ninfa, A.J.; Ballou, D.P.; Benore, M. |publisher=Wiley |year=2009 |pages=408–410 |isbn=9780470087664 |accessdate=08 April 2020}}</ref> and [[epidemiology]].<ref name="HamborskyEpidem15">{{cite book |title=Epidemiology and Prevention of Vaccine-Preventable Diseases |editor=Hamborsky, J.; Kroger, A.; Wolfe, C. |edition=13th |publisher=Centers for Disease Control and Prevention |year=2015 |url=https://www.cdc.gov/vaccines/pubs/pinkbook/index.html |accessdate=08 April 2020}}</ref>
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| PCR and its variations have been used to characterize and detect infectious disease organisms such as human immunodeficiency virus (HIV), pathogenic tuberculosis bacteria, and ''Bordetella pertussis'', which causes whooping cough.<ref name="BuckinghamMolec19">{{cite book |url=https://books.google.com/books?hl=en&lr=&id=dJWNDwAAQBAJ&pg=301 |chapter=Chapter 11: Detection and Identification of Microorganisms |title=Molecular Diagnostics: Fundamentals, Methods and Clinical Applications |author=Buckingham, L. |edition=3rd |pages=301–343 |year=2019 |publisher=F.A. Davis Company |isbn=9780803699540}}</ref> Additionally, a selection of viruses can have their RNA detected using PCR, though the primers (short single-strand DNA fragments) used in the process must by sympathetic to the virus' genetic structure to ensure that only target virus material is amplified.<ref name="KimMRPrimer17">{{cite journal |title=MRPrimerV: A database of PCR primers for RNA virus detection |journal=Nucleic Acids Research |author=Kim, H.; Kang, N.; An, K. et al. |volume=45 |issue=D1 |pages=D475–81 |year=2017 |doi=10.1093/nar/gkw1095 |pmid=27899620 |pmc=PMC5210568}}</ref> As it turns out, coronaviruses are RNA viruses, having some of the longest genomes of any RNA virus, and, detrimentally, the highest known frequency of recombination (the exchange of genetic material with another organism); this broadly means high rates of virus mutation, which interferes with maintaining consistent diagnostic detection and therapy.<ref name="MakinHowCorona20">{{cite web |url=https://www.scientificamerican.com/article/how-coronaviruses-cause-infection-from-colds-to-deadly-pneumonia1/ |title=How Coronaviruses Cause Infection—from Colds to Deadly Pneumonia |author=Makin, S. |work=Scientific American |date=05 February 2020 |accessdate=08 April 2020}}</ref><ref name="Rohde2019_20">{{cite web |url=https://asm.org/Articles/2020/January/2019-Novel-Coronavirus-2019-nCoV-Update-Uncoating |title=2019 Novel Coronavirus (2019-nCoV) Update: Uncoating the Virus |author=Rohde, R. |publisher=American Society for Microbiology |date=31 January 2020 |accessdate=08 April 2020}}</ref>
| | ==''Introduction to Quality and Quality Management Systems''== |
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| | | text = This book should not be considered complete until this message box has been removed. This is a work in progress. |
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| | 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. |
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| PCR comes in several variant methods. For example, while PCR monitors the amplification portion at the end of the overall process, real-time or "quantitative" PCR (qPCR) allows for the generation rate of the amplified product to be monitored at a particular point during each PCR cycle. Reverse transcription PCR (RT-PCR) is a combinatory process, applying reverse transcription (creating complementary double-stranded DNA [cDNA] from an RNA template) with PCR. If RT-PCR incorporates qPCR, you end up with "real-time RT-PCR" (rRT-PCR), sometimes referred to as "quantitative RT-PCR" (qRT-PCR). In the case of using PCR for detecting coronaviruses, more often than not we see some variation of RT-PCR, with or without real-time amplification monitoring. (It's important to not assume all RT-PCR processes incorporate real-time methods.)
| | ;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]] |
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| How does PCR work in practice? The simplified version (see this [https://doi.org/10.1001/jama.2020.5388 JAMA Patient Page] for a useful graphical explanation, using COVID-19 as an example) has a clinician obtaining a biological specimen from the appropriate location or source material. Then, special techniques are used to isolate viral (or in some cases, bacterial) genetic material from the specimen. (If RT-PCR is performed, the next step of reverse transcription of the isolated viral RNA into cDNA is also performed.) Once the viral genetic material is isolated, suitable primers that are sympathetic to the structure of the isolated genetic material are introduced. Those primers bind to the virus' genetic material and begin making copies of it. Fluorescent or other biomarkers that were attached to the copies during the PCR process eventually release from the copies, and an attempt is made to detect the presence of those biomarkers. The presence or absence of these markers drives the determination of a positive or negative detection for the sought-after virus.<ref name="HadayaTesting20">{{cite journal |title=Testing Individuals for Coronavirus Disease 2019 (COVID-19) |journal=JAMA |author=Hadaya, J.; Schumm, M.; Livingston, E.H. |year=2020 |doi=10.1001/jama.2020.5388 |pmid=32236503}}</ref>
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| ==References==
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