Misplaced Pages

Multiplex polymerase chain reaction: Difference between revisions

Article snapshot taken from[REDACTED] with creative commons attribution-sharealike license. Give it a read and then ask your questions in the chat. We can research this topic together.
Browse history interactively← Previous editContent deleted Content addedVisualWikitext
Revision as of 11:07, 27 March 2020 editIntgr (talk | contribs)Autopatrolled, Extended confirmed users, New page reviewers, Pending changes reviewers32,254 editsm Lead bold per MOS:LEADTag: Visual edit← Previous edit Latest revision as of 05:22, 9 June 2024 edit undoSafariScribe (talk | contribs)Extended confirmed users, Page movers, IP block exemptions, New page reviewers, Pending changes reviewers, Rollbackers81,796 edits Changing short description from "" to "Use of polymerase chain reaction to amplify several different DNA"Tag: Shortdesc helper 
(12 intermediate revisions by 7 users not shown)
Line 1: Line 1:
{{Short description|Use of polymerase chain reaction to amplify several different DNA}}
'''Multiplex polymerase chain reaction''' ('''Multiplex PCR''') refers to the use of ] to amplify several different DNA sequences simultaneously (as if performing many separate PCR reactions all together in one reaction). This process ] ] in samples using multiple ] and a temperature-mediated ] in a ]. The primer design for all primers pairs has to be optimized so that all primer pairs can work at the same annealing temperature during PCR. '''Multiplex polymerase chain reaction''' ('''Multiplex PCR''') refers to the use of ] to amplify several different DNA sequences simultaneously (as if performing many separate PCR reactions all together in one reaction). This process ] ] in samples using multiple ] and a temperature-mediated ] in a ]. The primer design for all primers pairs has to be optimized so that all primer pairs can work at the same annealing temperature during PCR.


Multiplex-PCR was first described in 1988 as a method to detect deletions in the ] gene.<ref>{{cite journal| journal=Nucleic Acids Research |title=Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification |vauthors=Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT |year=1988 |volume=16 |issue=23 |pages=11141–11156 |pmc=339001 |pmid=3205741 |doi=10.1093/nar/16.23.11141}}</ref> It has also been used with the ] gene.<ref>{{cite journal |title=Screening for steroid sulfatase (STS) gene deletions by multiplex DNA amplification |journal=Human Genetics |vauthors=Ballabio A, Ranier JE, Chamberlain JS, Zollo M, Caskey CT |volume=84 |issue=6 |pages=571–573 |year=1990 |pmid=2338343 |doi=10.1007/BF00210812|hdl=2027.42/47626 |url=https://deepblue.lib.umich.edu/bitstream/2027.42/47626/1/439_2004_Article_BF00210812.pdf }}</ref> In 2008, multiplex-PCR was used for analysis of ]s and ].<ref>{{cite journal |vauthors=Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ |title=Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping |journal=BMC Genomics |volume=9 |pages=80 |year=2008 |pmid=18282271 |pmc=2275739 |doi=10.1186/1471-2164-9-80 }}</ref> Multiplex-PCR was first described in 1988 as a method to detect deletions in the ] gene.<ref>{{cite journal| journal=Nucleic Acids Research |title=Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification |vauthors=Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT |year=1988 |volume=16 |issue=23 |pages=11141–11156 |pmc=339001 |pmid=3205741 |doi=10.1093/nar/16.23.11141}}</ref> It has also been used with the ] gene.<ref>{{cite journal |title=Screening for steroid sulfatase (STS) gene deletions by multiplex DNA amplification |journal=Human Genetics |vauthors=Ballabio A, Ranier JE, Chamberlain JS, Zollo M, Caskey CT |volume=84 |issue=6 |pages=571–573 |year=1990 |pmid=2338343 |doi=10.1007/BF00210812|hdl=2027.42/47626 |s2cid=18579745 |url=https://deepblue.lib.umich.edu/bitstream/2027.42/47626/1/439_2004_Article_BF00210812.pdf |hdl-access=free }}</ref> In 2008, multiplex-PCR was used for analysis of ]s and ].<ref>{{cite journal |vauthors=Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ |title=Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping |journal=BMC Genomics |volume=9 |pages=80 |year=2008 |pmid=18282271 |pmc=2275739 |doi=10.1186/1471-2164-9-80 |doi-access=free }}</ref> In 2020, RT-PCR multiplex assays were designed that combined multiple gene targets from the Center for Diseases and Control in a single reaction to increase molecular testing accessibility and throughput for ] diagnostics. <ref>{{cite journal|year=2020|last1=Perchetti|first1=GA| last2=Nalla|first2=AK| last3=Huang|first3=ML|last4=Jerome|first4=KR|last5=Greninger|first5=AL|author4-link=Keith R. Jerome|author5-link=Alexander L. Greninger|title=Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR|journal=Journal of Clinical Virology|volume=129|pages=104499|doi=10.1016/j.jcv.2020.104499|pmid=32535397|pmc=7278635|doi-access=free}}</ref>


Multiplex-PCR consists of multiple primer sets within a single PCR mixture to produce ]s of varying sizes that are specific to different DNA sequences. By targeting multiple sequences at once, additional information may be gained from a single test run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes, i.e., their base pair length, should be different enough to form distinct bands when visualized by ]. Alternatively, if amplicon sizes overlap, the different amplicons may be differentiated and visualised using primers that have been dyed with different colour fluorescent dyes. Commercial multiplexing kits for PCR are available and used by many forensic laboratories to amplify degraded DNA samples. Multiplex-PCR consists of multiple primer sets within a single PCR mixture to produce ]s of varying sizes that are specific to different DNA sequences. By targeting multiple sequences at once, additional information may be gained from a single test run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes, i.e., their base pair length, should be different enough to form distinct bands when visualized by ]. Alternatively, if amplicon sizes overlap, the different amplicons may be differentiated and visualised using primers that have been dyed with different colour fluorescent dyes. Commercial multiplexing kits for PCR are available and used by many forensic laboratories to amplify degraded DNA samples.


== Applications == == Applications ==
Some of the ] of multiplex PCR include: Some of the ] of multiplex PCR include:
# Pathogen Identification<ref>{{cite journal |doi=10.1186/1471-2180-9-161|pmid=19664269|pmc=2741468|title=Rapid identification of bacterial pathogens using a PCR- and microarray-based assay|journal=BMC Microbiology|volume=9|pages=161|year=2009|last1=Järvinen|first1=Anna-Kaarina|last2=Laakso|first2=Sanna|last3=Piiparinen|first3=Pasi|last4=Aittakorpi|first4=Anne|last5=Lindfors|first5=Merja|last6=Huopaniemi|first6=Laura|last7=Piiparinen|first7=Heli|last8=Mäki|first8=Minna}}</ref> # Pathogen Identification<ref>{{cite journal |doi=10.1186/1471-2180-9-161|pmid=19664269|pmc=2741468|title=Rapid identification of bacterial pathogens using a PCR- and microarray-based assay|journal=BMC Microbiology|volume=9|pages=161|year=2009|last1=Järvinen|first1=Anna-Kaarina|last2=Laakso|first2=Sanna|last3=Piiparinen|first3=Pasi|last4=Aittakorpi|first4=Anne|last5=Lindfors|first5=Merja|last6=Huopaniemi|first6=Laura|last7=Piiparinen|first7=Heli|last8=Mäki|first8=Minna |doi-access=free }}</ref>
# High Throughput SNP Genotyping<ref>{{Cite journal | url=http://genome.cshlp.org/content/11/1/163.full | doi=10.1101/gr.157901| pmid=11156625| title=High-Throughput SNP Genotyping by Allele-Specific PCR with Universal Energy-Transfer-Labeled Primers| journal=Genome Research| volume=11| pages=163–169| year=2001| last1=Myakishev| first1=M. V.| issue=1| pmc=311033}}</ref> # High Throughput SNP Genotyping<ref>{{Cite journal | doi=10.1101/gr.157901| pmid=11156625| title=High-Throughput SNP Genotyping by Allele-Specific PCR with Universal Energy-Transfer-Labeled Primers| journal=Genome Research| volume=11| pages=163–169| year=2001| last1=Myakishev| first1=M. V.| issue=1| pmc=311033}}</ref>
# Mutation Analysis<ref>{{cite journal |doi=10.1371/journal.pone.0004584|pmid=19240792|title=Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method|journal=PLOS ONE|volume=4|issue=2|pages=e4584|year=2009|last1=Morlan|first1=John|last2=Baker|first2=Joffre|last3=Sinicropi|first3=Dominick|bibcode=2009PLoSO...4.4584M|pmc=2642996}}</ref> # Mutation Analysis<ref>{{cite journal |doi=10.1371/journal.pone.0004584|pmid=19240792|title=Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method|journal=PLOS ONE|volume=4|issue=2|pages=e4584|year=2009|last1=Morlan|first1=John|last2=Baker|first2=Joffre|last3=Sinicropi|first3=Dominick|bibcode=2009PLoSO...4.4584M|pmc=2642996|doi-access=free}}</ref>
# Gene Deletion Analysis<ref>{{cite journal |pmc=1015896|year=1992|last1=Abbs|first1=S|title=Analysis of quantitative PCR for the diagnosis of deletion and duplication carriers in the dystrophin gene|journal=Journal of Medical Genetics|volume=29|issue=3|pages=191–196|last2=Bobrow|first2=M|doi=10.1136/jmg.29.3.191|pmid=1552558}}</ref> # Gene Deletion Analysis<ref>{{cite journal |pmc=1015896|year=1992|last1=Abbs|first1=S|title=Analysis of quantitative PCR for the diagnosis of deletion and duplication carriers in the dystrophin gene|journal=Journal of Medical Genetics|volume=29|issue=3|pages=191–196|last2=Bobrow|first2=M|doi=10.1136/jmg.29.3.191|pmid=1552558}}</ref>
# Template Quantitation<ref>{{cite web | url=http://dna.fiu.edu/Advanced%20DNA%20Typing%20lectures/An%20introduction%20to%20principles%20of%20QPCR-D.pdf | title=Welcome &#124; Forensic DNA Profiling Facility}}</ref> # Template Quantitation<ref>{{cite web | url=http://dna.fiu.edu/Advanced%20DNA%20Typing%20lectures/An%20introduction%20to%20principles%20of%20QPCR-D.pdf | title=Welcome &#124; Forensic DNA Profiling Facility}}</ref>
Line 15: Line 16:
# RNA Detection<ref>{{Cite journal | title=Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5'-noncoding region| journal=The Japanese Journal of Experimental Medicine| volume=60| issue=4| pages=215–222| date=August 1990| last1=Miyakawa| first1=Y.| last2=Yoshizawa| first2=H.| last3=Mishiro| first3=S.| last4=Machida| first4=A.| last5=Akahane| first5=Y.| last6=Sugai| first6=Y.| last7=Tanaka| first7=T.| last8=Sugiyama| first8=Y.| last9=Okada| first9=S.| last10=Okamoto| first10=H.|pmid = 1963453}}</ref> # RNA Detection<ref>{{Cite journal | title=Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5'-noncoding region| journal=The Japanese Journal of Experimental Medicine| volume=60| issue=4| pages=215–222| date=August 1990| last1=Miyakawa| first1=Y.| last2=Yoshizawa| first2=H.| last3=Mishiro| first3=S.| last4=Machida| first4=A.| last5=Akahane| first5=Y.| last6=Sugai| first6=Y.| last7=Tanaka| first7=T.| last8=Sugiyama| first8=Y.| last9=Okada| first9=S.| last10=Okamoto| first10=H.|pmid = 1963453}}</ref>
# Forensic Studies<ref>{{cite web | url=https://nij.gov/topics/forensics/evidence/dna/basics/pages/analyzing.aspx | title=DNA Evidence: Basics of Analyzing}}</ref> # Forensic Studies<ref>{{cite web | url=https://nij.gov/topics/forensics/evidence/dna/basics/pages/analyzing.aspx | title=DNA Evidence: Basics of Analyzing}}</ref>
# Diet Analysis<ref>{{cite journal |doi=10.1371/journal.pone.0005252|pmid=19390570|pmc=2668750|title=DNA-Based Diet Analysis for Any Predator|journal=PLOS ONE|volume=4|issue=4|pages=e5252|year=2009|last1=Dunshea|first1=Glenn|bibcode=2009PLoSO...4.5252D}}</ref> # Diet Analysis<ref>{{cite journal |doi=10.1371/journal.pone.0005252|pmid=19390570|pmc=2668750|title=DNA-Based Diet Analysis for Any Predator|journal=PLOS ONE|volume=4|issue=4|pages=e5252|year=2009|last1=Dunshea|first1=Glenn|bibcode=2009PLoSO...4.5252D|doi-access=free}}</ref>


==References== ==References==

Latest revision as of 05:22, 9 June 2024

Use of polymerase chain reaction to amplify several different DNA

Multiplex polymerase chain reaction (Multiplex PCR) refers to the use of polymerase chain reaction to amplify several different DNA sequences simultaneously (as if performing many separate PCR reactions all together in one reaction). This process amplifies DNA in samples using multiple primers and a temperature-mediated DNA polymerase in a thermal cycler. The primer design for all primers pairs has to be optimized so that all primer pairs can work at the same annealing temperature during PCR.

Multiplex-PCR was first described in 1988 as a method to detect deletions in the dystrophin gene. It has also been used with the steroid sulfatase gene. In 2008, multiplex-PCR was used for analysis of microsatellites and SNPs. In 2020, RT-PCR multiplex assays were designed that combined multiple gene targets from the Center for Diseases and Control in a single reaction to increase molecular testing accessibility and throughput for SARS-CoV-2 diagnostics.

Multiplex-PCR consists of multiple primer sets within a single PCR mixture to produce amplicons of varying sizes that are specific to different DNA sequences. By targeting multiple sequences at once, additional information may be gained from a single test run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes, i.e., their base pair length, should be different enough to form distinct bands when visualized by gel electrophoresis. Alternatively, if amplicon sizes overlap, the different amplicons may be differentiated and visualised using primers that have been dyed with different colour fluorescent dyes. Commercial multiplexing kits for PCR are available and used by many forensic laboratories to amplify degraded DNA samples.

Applications

Some of the applications of multiplex PCR include:

  1. Pathogen Identification
  2. High Throughput SNP Genotyping
  3. Mutation Analysis
  4. Gene Deletion Analysis
  5. Template Quantitation
  6. Linkage Analysis
  7. RNA Detection
  8. Forensic Studies
  9. Diet Analysis

References

  1. Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT (1988). "Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification". Nucleic Acids Research. 16 (23): 11141–11156. doi:10.1093/nar/16.23.11141. PMC 339001. PMID 3205741.
  2. Ballabio A, Ranier JE, Chamberlain JS, Zollo M, Caskey CT (1990). "Screening for steroid sulfatase (STS) gene deletions by multiplex DNA amplification" (PDF). Human Genetics. 84 (6): 571–573. doi:10.1007/BF00210812. hdl:2027.42/47626. PMID 2338343. S2CID 18579745.
  3. Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ (2008). "Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping". BMC Genomics. 9: 80. doi:10.1186/1471-2164-9-80. PMC 2275739. PMID 18282271.
  4. Perchetti, GA; Nalla, AK; Huang, ML; Jerome, KR; Greninger, AL (2020). "Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR". Journal of Clinical Virology. 129: 104499. doi:10.1016/j.jcv.2020.104499. PMC 7278635. PMID 32535397.
  5. Järvinen, Anna-Kaarina; Laakso, Sanna; Piiparinen, Pasi; Aittakorpi, Anne; Lindfors, Merja; Huopaniemi, Laura; Piiparinen, Heli; Mäki, Minna (2009). "Rapid identification of bacterial pathogens using a PCR- and microarray-based assay". BMC Microbiology. 9: 161. doi:10.1186/1471-2180-9-161. PMC 2741468. PMID 19664269.
  6. Myakishev, M. V. (2001). "High-Throughput SNP Genotyping by Allele-Specific PCR with Universal Energy-Transfer-Labeled Primers". Genome Research. 11 (1): 163–169. doi:10.1101/gr.157901. PMC 311033. PMID 11156625.
  7. Morlan, John; Baker, Joffre; Sinicropi, Dominick (2009). "Mutation Detection by Real-Time PCR: A Simple, Robust and Highly Selective Method". PLOS ONE. 4 (2): e4584. Bibcode:2009PLoSO...4.4584M. doi:10.1371/journal.pone.0004584. PMC 2642996. PMID 19240792.
  8. Abbs, S; Bobrow, M (1992). "Analysis of quantitative PCR for the diagnosis of deletion and duplication carriers in the dystrophin gene". Journal of Medical Genetics. 29 (3): 191–196. doi:10.1136/jmg.29.3.191. PMC 1015896. PMID 1552558.
  9. "Welcome | Forensic DNA Profiling Facility" (PDF).
  10. Reis, Andre (1991). "PCR in Linkage Analysis of Genetic Diseases". PCR Topics. pp. 75–79. doi:10.1007/978-3-642-75924-6_15. ISBN 978-3-540-52934-7.
  11. Miyakawa, Y.; Yoshizawa, H.; Mishiro, S.; Machida, A.; Akahane, Y.; Sugai, Y.; Tanaka, T.; Sugiyama, Y.; Okada, S.; Okamoto, H. (August 1990). "Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5'-noncoding region". The Japanese Journal of Experimental Medicine. 60 (4): 215–222. PMID 1963453.
  12. "DNA Evidence: Basics of Analyzing".
  13. Dunshea, Glenn (2009). "DNA-Based Diet Analysis for Any Predator". PLOS ONE. 4 (4): e5252. Bibcode:2009PLoSO...4.5252D. doi:10.1371/journal.pone.0005252. PMC 2668750. PMID 19390570.
Polymerase chain reaction techniques
Procedure
Polymerase
Optimization
and variants
History
and people
Portal: Categories:
Multiplex polymerase chain reaction: Difference between revisions Add topic