Skip to main content

Real-Time PCR and Multiplex Approaches

  • Protocol
  • First Online:
Book cover Gene Expression Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 784))

Abstract

Analysis of RNA expression levels by real-time reverse-transcription (RT) PCR has become a routine technique in diagnostic and research laboratories. Monitoring of DNA amplification can be done using fluorescent sequence-specific probes, which generate signal only upon binding to their target. Numerous fluorescent dyes with unique emission spectra are available and can be used to differentially label probes for various genes. Such probes can be added to the same PCR amplification reaction for simultaneous detection of multiple targets in a single assay. Such multiplexing is advantageous, since it markedly increases throughput and decreases costs and labor. Here, we describe application of multiplex real-time RT-PCR using TaqMan probes in the analysis of relative expression levels of a novel tumor-associated gene CUG2 in cell lines and tissue samples.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 59.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 79.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Murphy, J. and Bustin, S.A. (2009) Reliability of real-time reverse-transcription PCR in clinical diagnostics: gold standard or substandard? Expert Review of Molecular Diagnostics, 9, 187–197.

    Article  PubMed  CAS  Google Scholar 

  2. Schmittgen, T.D., Lee, E.J., Jiang, J., Sarkar, A., Yang, L., Elton, T.S. and Chen, C. (2008) Real-time PCR quantification of precursor and mature microRNA. Methods (San Diego, Calif), 44, 31–38.

    Google Scholar 

  3. Koga, T., Tokunaga, E., Sumiyoshi, Y., Oki, E., Oda, S., Takahashi, I., Kakeji, Y., Baba, H. and Maehara, Y. (2008) Detection of circulating gastric cancer cells in peripheral blood using real time quantitative RT-PCR. Hepato-gastroenterology, 55, 1131–1135.

    PubMed  CAS  Google Scholar 

  4. Rizzi, F., Belloni, L., Crafa, P., Lazzaretti, M., Remondini, D., Ferretti, S., Cortellini, P., Corti, A. and Bettuzzi, S. (2008) A novel gene signature for molecular diagnosis of human prostate cancer by RT-qPCR. PloS One, 3, e3617.

    Article  PubMed  Google Scholar 

  5. Pignot, G., Bieche, I., Vacher, S., Guet, C., Vieillefond, A., Debre, B., Lidereau, R. and Amsellem-Ouazana, D. (2009) Large-scale real-time reverse transcription-PCR approach of angiogenic pathways in human transitional cell carcinoma of the bladder: identification of VEGFA as a major independent prognostic marker. European Urology, 56, 678–688.

    Article  PubMed  CAS  Google Scholar 

  6. Andreeff, M., Ruvolo, V., Gadgil, S., Zeng, C., Coombes, K., Chen, W., Kornblau, S., Baron, A.E. and Drabkin, H.A. (2008) HOX expression patterns identify a common signature for favorable AML. Leukemia, 22, 2041–2047.

    Article  PubMed  CAS  Google Scholar 

  7. Wakeley, P.R., Johnson, N., McElhinney, L.M., Marston, D., Sawyer, J. and Fooks, A.R. (2005) Development of a real-time, TaqMan reverse transcription-PCR assay for detection and differentiation of lyssavirus genotypes 1, 5, and 6. Journal of Clinical Microbiology, 43, 2786–2792.

    Article  PubMed  CAS  Google Scholar 

  8. Lu, X., Holloway, B., Dare, R.K., Kuypers, J., Yagi, S., Williams, J.V., Hall, C.B. and Erdman, D.D. (2008) Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses. Journal of Clinical Microbiology, 46, 533–539.

    Article  PubMed  CAS  Google Scholar 

  9. Wang, L., Giannoudis, A., Lane, S., Williamson, P., Pirmohamed, M. and Clark, R.E. (2008) Expression of the uptake drug transporter hOCT1 is an important clinical determinant of the response to imatinib in chronic myeloid leukemia. Clinical Pharmacology and Therapeutics, 83, 258–264.

    Article  PubMed  CAS  Google Scholar 

  10. Mischitelli, M., Fioriti, D., Anzivino, E., Bellizzi, A., Ferretti, G., Gussman, N., Mitterhofer, A.P., Tinti, F., Barile, M., Dal Maso, M. et al.(2007) BKV QPCR detection and infection monitoring in renal transplant recipients. New Microbiol, 30, 271–274.

    PubMed  Google Scholar 

  11. Mackay, J. and Landt, O. (2007) Real-time PCR fluorescent chemistries. Methods in Molecular Biology (Clifton, N.J) 353, 237–261.

    Google Scholar 

  12. Gibson, U.E., Heid, C.A. and Williams, P.M. (1996) A novel method for real time quantitative RT-PCR. Genome Research, 6, 995–1001.

    Article  PubMed  CAS  Google Scholar 

  13. Tyagi, S. and Kramer, F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology, 14, 303–308.

    Article  PubMed  CAS  Google Scholar 

  14. Whitcombe, D., Theaker, J., Guy, S.P., Brown, T. and Little, S. (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nature Biotechnology, 17, 804–807.

    Article  PubMed  CAS  Google Scholar 

  15. Thelwell, N., Millington, S., Solinas, A., Booth, J. and Brown, T. (2000) Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Research, 28, 3752–3761.

    Article  PubMed  CAS  Google Scholar 

  16. Lee, S., Gang, J., Jeon, S.B., Choo, S.H., Lee, B., Kim, Y.G., Lee, Y.S., Jung, J., Song, S.Y. and Koh, S.S. (2007) Molecular cloning and functional analysis of a novel oncogene, cancer-upregulated gene 2 (CUG2). Biochemical and Biophysical Research Communications, 360, 633–639.

    Article  PubMed  CAS  Google Scholar 

  17. Kim, H., Lee, M., Lee, S., Park, B., Koh, W., Lee, D.J., Lim, D.S. and Lee, S. (2009) Cancer-upregulated gene 2 (CUG2), a new component of centromere complex, is required for kinetochore function. Molecules and Cells, 27, 697–701.

    Article  PubMed  CAS  Google Scholar 

  18. de Kok, J.B., Roelofs, R.W., Giesendorf, B.A., Pennings, J.L., Waas, E.T., Feuth, T., Swinkels, D.W. and Span, P.N. (2005) Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Laboratory Investigation; a Journal of Technical Methods and Pathology, 85, 154–159.

    Google Scholar 

  19. Gresner, P., Gromadzinska, J. and Wasowicz, W. (2009) Reference genes for gene expression studies on non-small cell lung cancer. Acta Biochimica Polonica, 56, 307–316.

    PubMed  CAS  Google Scholar 

  20. Pernot, F., Dorandeu, F., Beaup, C. and Peinnequin, A. (2010) Selection of reference genes for real-time quantitative reverse transcription-polymerase chain reaction in hippocampal structure in a murine model of temporal lobe epilepsy with focal seizures. Journal of Neuroscience Research, 8, 1000–1008.

    Google Scholar 

  21. Taveau, M., Stockholm, D., Spencer, M. and Richard, I. (2002) Quantification of splice variants using molecular beacon or scorpion primers. Analytical Biochemistry, 305, 227–235.

    Article  PubMed  CAS  Google Scholar 

  22. Roux, K.H. (2002) Single-step PCR optimization using touchdown and stepdown PCR ­programming. Methods in Molecular Biology (Clifton, N.J.), 192, 31–36.

    Google Scholar 

Download references

Acknowledgments

Authors would like to thank Alexander Skoblov and Michelle Nyhan for their help and advice in preparation of the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Olga L. Gurvich .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Gurvich, O.L., Skoblov, M. (2011). Real-Time PCR and Multiplex Approaches. In: O'Driscoll, L. (eds) Gene Expression Profiling. Methods in Molecular Biology, vol 784. Humana Press. https://doi.org/10.1007/978-1-61779-289-2_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-289-2_1

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-288-5

  • Online ISBN: 978-1-61779-289-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics