Quantitative Real-Time PCR: Recent Advances

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Clinical Applications of PCR

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1392))

Abstract

Quantitative real-time polymerase chain reaction is a technique for simultaneous amplification and product quantification of a target DNA as the process takes place in real time in a “closed-tube” system. Although this technique can provide an absolute quantification of the initial template copy number, quantification relative to a control sample or second sequence is typically adequate. The quantification process employs melting curve analysis and/or fluorescent detection systems and can provide amplification and genoty** in a relatively short time. Here we describe the properties and uses of various fluorescent detection systems used for quantification.

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References

  1. Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):611–622

    Article  CAS  PubMed  Google Scholar 

  2. Nolan T, Hands RE, Bustin SA (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1(3):1559–1582

    Article  CAS  PubMed  Google Scholar 

  3. Burns MJ, Nixon GJ, Foy CA et al (2005) Standardisation of data from real-time quantitative PCR methods – evaluation of outliers and comparison of calibration curves. BMC Biotechnol 5:31

    Article  PubMed Central  PubMed  Google Scholar 

  4. Huggett J, Dheda K, Bustin S et al (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6(4):279–284

    Article  CAS  PubMed  Google Scholar 

  5. Ririe KM, Rasmussen RP, Wittwer CT (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 245(2):154–160

    Article  CAS  PubMed  Google Scholar 

  6. Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50(10):1748–1754

    Article  CAS  PubMed  Google Scholar 

  7. Pryor RJ, Wittwer CT (2006) Real-time polymerase chain reaction and melting curve analysis. Methods Mol Biol 336:19–32

    CAS  PubMed  Google Scholar 

  8. Mitsuhashi M (1996) Technical report: part 2. Basic requirements for designing optimal PCR primers. J Clin Lab Anal 10(5):285–293

    Article  CAS  PubMed  Google Scholar 

  9. Haas SA, Hild M, Wright AP et al (2003) Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 31(19):5576–5581

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Sugimoto N, Nakano S, Yoneyama M et al (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24(22):4501–4505

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Rychlik W, Spencer WJ, Rhoads RE (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res 18(21):6409–6412

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37(2):226–231

    CAS  PubMed  Google Scholar 

  13. Mount DW (2007) Using the basic local alignment search tool (BLAST). CSH Protocol. pdb top17

    Google Scholar 

  14. Sherry ST, Ward MH, Kholodov M et al (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29(1):308–311

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Giglio S, Monis PT, Saint CP (2003) Demonstration of preferential binding of SYBR Green I to specific DNA fragments in real-time multiplex PCR. Nucleic Acids Res 31(22): e136

    Article  PubMed Central  PubMed  Google Scholar 

  16. Bengtsson M, Karlsson HJ, Westman G et al (2003) A new minor groove binding asymmetric cyanine reporter dye for real-time PCR. Nucleic Acids Res 31(8):e45

    Article  PubMed Central  PubMed  Google Scholar 

  17. Morrison TB, Weis JJ, Wittwer CT (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechniques 24(6):954–958

    CAS  PubMed  Google Scholar 

  18. Ram S, Singh RL, Shanker R (2008) In silico comparison of real-time PCR probes for detection of pathogens. In Silico Biol 8(3–4):251–259

    CAS  PubMed  Google Scholar 

  19. Simon A, Labalette P, Ordinaire I et al (2004) Use of fluorescence resonance energy transfer hybridization probes to evaluate quantitative real-time PCR for diagnosis of ocular toxoplasmosis. J Clin Microbiol 42(8):3681–3685

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Johansson MK (2006) Choosing reporter-quencher pairs for efficient quenching through formation of intramolecular dimers. Methods Mol Biol 335:17–29

    CAS  PubMed  Google Scholar 

  21. Wittwer CT, Herrmann MG, Moss AA et al (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22(1):130–131

    CAS  PubMed  Google Scholar 

  22. Kostrikis LG, Tyagi S, Mhlanga MM et al (1998) Spectral genoty** of human alleles. Science 279(5354):1228–1229

    Article  CAS  PubMed  Google Scholar 

  23. Tyagi S, Kramer FR (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14(3):303–308

    Article  CAS  PubMed  Google Scholar 

  24. Fang X, Li JJ, Perlette J, Tan W et al (2002) Molecular beacons: novel fluorescent probes. Anal Chem 72(23):747A–753A

    Google Scholar 

  25. Lyon E, Wittwer CT (2009) LightCycler technology in molecular diagnostics. J Mol Diagn 11(2):93–101

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Wittwer CT, Ririe KM, Andrew RV et al (1997) The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques 22(1):176–181

    CAS  PubMed  Google Scholar 

  27. Vu HL, Troubetzkoy S, Nguyen HH et al (2000) A method for quantification of absolute amounts of nucleic acids by (RT)-PCR and a new mathematical model for data analysis. Nucleic Acids Res 28(7):E18

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Regier N, Frey B (2010) Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar. BMC Mol Biol 11:57

    Article  PubMed Central  PubMed  Google Scholar 

  29. Bustin SA, Mueller R (2005) Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci 109(4):365–379

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Sinchita Roy-Chowdhuri .

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Singh, C., Roy-Chowdhuri, S. (2016). Quantitative Real-Time PCR: Recent Advances. In: Luthra, R., Singh, R., Patel, K. (eds) Clinical Applications of PCR. Methods in Molecular Biology, vol 1392. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3360-0_15

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  • DOI: https://doi.org/10.1007/978-1-4939-3360-0_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3358-7

  • Online ISBN: 978-1-4939-3360-0

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