Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-8448b6f56d-t5pn6 Total loading time: 0 Render date: 2024-04-24T14:26:33.663Z Has data issue: false hasContentIssue false

Chapter 5 - Clinical applications of the polymerase chain reaction for molecular pathology

Published online by Cambridge University Press:  05 November 2015

By
Angela B. Y. Hui ,
Annette D. Wong  and
Carlo V. Hojilla
Edited by
John M. S. Bartlett ,
Abeer Shaaban  and
Fernando Schmitt
John M. S. Bartlett
Affiliation:
Ontario Institute for Cancer Research, Toronto
Abeer Shaaban
Affiliation:
Queen Elizabeth Hospital Birmingham
Fernando Schmitt
Affiliation:
University of Porto
Get access
Type
Chapter
Information
Molecular Pathology
A Practical Guide for the Surgical Pathologist and Cytopathologist
 , pp. 55 - 70
Publisher: Cambridge University Press
Print publication year: 2015

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G. and Erlich, H. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 1986; 51(Pt 1): 263–73.CrossRefGoogle ScholarPubMed
Hunt, J. L. Molecular pathology in anatomic pathology practice: a review of basic principles. Arch Pathol Lab Med 2008; 132(2): 248–60.CrossRefGoogle Scholar
Gonzalez-Angulo, A. M., Hennessy, B. T. and Mills, G. B. Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol 2010; 28(16): 2777–83.CrossRefGoogle Scholar
Bossler, A. and van Deerlin, V. Conventional and real-time polymerase chain reaction, in Tubbs, R. R. and Stoler, M. H. (eds.), Cell and Tissue Based Molecular Pathology (Philadelphia, PA: Churchill Livingstone Elsevier Inc., 2009), pp. 33–49.CrossRefGoogle Scholar
Rennert, H. and Leonard, D. G. B., Molecular methods in the diagnostic laboratory, in Leonard, D. G. B. (ed.), Diagnostic Molecular Pathology (Philadelphia, PA: Saunders, 2003), pp. 25–52.Google Scholar
Coleman, W. G. and Tsongalis, G. J. Essential Concepts in Molecular Pathology (San Diego, CA: Elsevier, 2010).Google Scholar
Lo, Y. M. and Chan, K. C. Setting up a polymerase chain reaction laboratory. Methods Mol Biol 2006; 336:11–18.Google Scholar
Remick, D. G., Kunkel, S. L., Holbrook, E. A. and Hanson, C. A. Theory and applications of the polymerase chain reaction. Am J Clin Pathol 1990; 93(4 Suppl. 1): S49–54.Google Scholar
Mies, C. Molecular biological analysis of paraffin-embedded tissues. Hum Pathol 1994; 25(6): 555–60.CrossRefGoogle ScholarPubMed
Farkas, D. H. and Holland, C. A. Overview of molecular diagnostic techniques and instrumentation, in Tubbs, R. R. and Stoler, M. H. (eds.), Cell and Tissue Based Molecular Pathology (Philadelphia, PA: Churchill Livingstone Elsevier Inc, 2009), pp. 19–35.CrossRefGoogle Scholar
Baumforth, K. R., Nelson, P. N., Digby, J. E., O'Neil, J. D. and Murray, P. G. Demystified … the polymerase chain reaction. Mol Pathol 1999; 52(1): 1–10.CrossRefGoogle ScholarPubMed
Ririe, K. M., Rasmussen, R. P. and Wittwer, C. T. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal Biochem 1997; 245(2): 154–60.CrossRefGoogle ScholarPubMed
Wienken, C. J., Baaske, P., Duhr, S. and Braun, D. Thermophoretic melting curves quantify the conformation and stability of RNA and DNA. Nucleic Acids Res 2011; 39(8): e52.CrossRefGoogle ScholarPubMed
Joyce, C. Quantitative RT-PCR. A review of current methodologies. Methods Mol Biol 2002; 193: 83–92.Google ScholarPubMed
Oliver, D. Polymerase chain reaction and reverse transcription-polymerase chain reaction, in Cagle, P. T. and Allen, T. C. (eds.), Basic Concepts of Molecular Pathology (New York: Springer, 2009), pp. 73–85.CrossRefGoogle Scholar
Deepak, S., Kottapalli, K., Rakwal, R., Oros, G., Rangappa, K., Iwahashi, H. et al. Real-time PCR: revolutionizing detection and expression analysis of genes. Curr Genomics 2007; 8(4): 234–51.CrossRefGoogle ScholarPubMed
Freeman, W. M., Walker, S. J. and Vrana, K. E. Quantitative RT-PCR: pitfalls and potential. Biotechniques 1999; 26(1): 112–22, 24–5.CrossRefGoogle ScholarPubMed
Whitcombe, D., Theaker, J., Guy, S. P., Brown, T. and Little, S. Detection of PCR products using self-probing amplicons and fluorescence. Nat Biotechnol 1999; 17(8): 804–7.CrossRefGoogle ScholarPubMed
Edwards, M. C. and Gibbs, R. A. Multiplex PCR: advantages, development, and applications. PCR Methods Appl 1994; 3(4): S65–75.CrossRefGoogle ScholarPubMed
Homig-Holzel, C. and Savola, S. Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics. Diagn Mol Pathol 2012; 21(4): 189–206.CrossRefGoogle ScholarPubMed
Vogelstein, B. and Kinzler, K. W. Digital PCR. Proc Natl Acad Sci USA 1999; 96(16): 9236–41.CrossRefGoogle ScholarPubMed
Day, E., Dear, P. H. and McCaughan, F. Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 2013; 59(1): 101–7.CrossRefGoogle ScholarPubMed
McCaughan, F. and Dear, P. H. Single-molecule genomics. J Pathol 2010; 220(2): 297–306.CrossRefGoogle ScholarPubMed
Killeen, A. A. Principles of Molecular Pathology (Totowa, NJ: Humana Press, 2004).CrossRefGoogle Scholar
Lo, Y. M. and Chan, K. C. Introduction to the polymerase chain reaction. Methods Mol Biol 2006; 336: 1–10.Google ScholarPubMed
Sanger, F., Nicklen, S. and Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12): 5463–7.CrossRefGoogle ScholarPubMed
Bernard, P. S. and Wittwer, C. T. Real-time PCR technology for cancer diagnostics. Clin Chem 2002; 48(8): 1178–85.CrossRefGoogle ScholarPubMed
Crocker, J. Demystified … molecular pathology in oncology. Mol Pathol 2002; 55(6): 337–47.CrossRefGoogle ScholarPubMed
Thompson, R., Zoppis, S. and McCord, B. An overview of DNA typing methods for human identification: past, present, and future. Methods Mol Biol 2012; 830: 3–16.CrossRefGoogle ScholarPubMed
McCourt, C. M., McArt, D. G., Mills, K., Catherwood, M. A., Maxwell, P., Waugh, D. J. et al. Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS ONE 2013; 8(7): e69604.CrossRefGoogle ScholarPubMed
Goswami, R. S., Waldron, L., Machado, J., Cervigne, N. K., Xu, W., Reis, P. P. et al. Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples. BMC Biotechnol 2010; 10: 47.CrossRefGoogle ScholarPubMed
Goel, A., Nagasaka, T., Hamelin, R. and Boland, C. R. An optimized pentaplex PCR for detecting DNA mismatch repair-deficient colorectal cancers. PLoS ONE 2010; 5(2): e9393.CrossRefGoogle ScholarPubMed
Lin, M. T., Tseng, L. H., Rich, R. G., Hafez, M. J., Harada, S., Murphy, K. M. et al. Delta-PCR, a simple method to detect translocations and insertion/deletion mutations. J Mol Diagn 2011; 13(1): 85–92.CrossRefGoogle ScholarPubMed
Chaturbedi, A., Yu, L., Linskey, M. E. and Zhou, Y. H. Detection of 1p19q deletion by real-time comparative quantitative PCR. Biomark Insights 2012; 7: 9–17.CrossRefGoogle ScholarPubMed
Liu, H., Bench, A. J., Bacon, C. M., Payne, K., Huang, Y., Scott, M. A. et al. A practical strategy for the routine use of BIOMED-2 PCR assays for detection of B- and T-cell clonality in diagnostic haematopathology. Br J Haematol 2007; 138(1): 31–43.CrossRefGoogle ScholarPubMed
Lindemann, M. L., Dominguez, M. J., de Antonio, J. C., Sandri, M. T., Tricca, A., Sideri, M. et al. Analytical comparison of the cobas HPV Test with Hybrid Capture 2 for the detection of high-risk HPV genotypes. J Mol Diagn 2012; 14(1): 65–70.CrossRefGoogle ScholarPubMed
Thijsen, S. F. and Deege, M. P. Molecular diagnosis of Epstein-Barr virus infections. Expert Opin Med Diagn 2008; 2(1): 21–31.CrossRefGoogle ScholarPubMed
van der Velden, V. H., Hochhaus, A., Cazzaniga, G., Szczepanski, T., Gabert, J. and van Dongen, J. J. Detection of minimal residual disease in hematologic malignancies by real-time quantitative PCR: principles, approaches, and laboratory aspects. Leukemia 2003; 17(6): 1013–34.CrossRefGoogle ScholarPubMed
Onay, H., Ugurlu, T., Aykut, A., Pehlivan, S., Inal, M., Tinar, S. et al. Rapid prenatal diagnosis of common aneuploidies in amniotic fluid using quantitative fluorescent polymerase chain reaction. Gynecol Obstet Invest 2008; 66(2): 104–10.CrossRefGoogle ScholarPubMed
Shan, L., Rabi, S. A., Laird, G. M., Eisele, E. E., Zhang, H., Margolick, J. B. et al. A novel PCR assay for quantification of HIV-1 RNA. J Virol 2013; 87(11): 6521–5.CrossRefGoogle ScholarPubMed
Park, K. S., Kim, J. Y., Lee, J. W., Hwang, Y. Y., Jeon, K., Koh, W. J. et al. Comparison of the Xpert MTB/RIF and Cobas TaqMan MTB assays for detection of mycobacterium tuberculosis in respiratory specimens. J Clin Microbiol 2013; 51(10): 3225–7.CrossRefGoogle ScholarPubMed
Procter, M., Chou, L. S., Tang, W., Jama, M. and Mao, R. Molecular diagnosis of Prader-Willi and Angelman syndromes by methylation-specific melting analysis and methylation-specific multiplex ligation-dependent probe amplification. Clin Chem 2006; 52(7): 1276–83.CrossRefGoogle ScholarPubMed
Igbokwe, A. and Lopez-Terrada, D. H. Molecular testing of solid tumors. Arch Pathol Lab Med 2011; 135(1): 67–82.CrossRefGoogle ScholarPubMed
Allen, T. C., Cagle, P. T. and Popper, H. H. Basic concepts of molecular pathology. Arch Pathol Lab Med 2008; 132(10): 1551–6.CrossRefGoogle ScholarPubMed
Pickl, M., Ruge, E. and Venturi, M. Predictive markers in early research and companion diagnostic developments in oncology. N Biotechnol 2012; 29(6): 651–5.CrossRefGoogle ScholarPubMed
Kittaneh, M., Montero, A. J. and Gluck, S. Molecular profiling for breast cancer: a comprehensive review. Biomark Cancer 2013; 5: 61–70.CrossRefGoogle ScholarPubMed
Ross, J. S. Multigene classifiers, prognostic factors, and predictors of breast cancer clinical outcome. Adv Anat Pathol 2009; 16(4): 204–15.CrossRefGoogle ScholarPubMed
Dowsett, M., Sestak, I., Lopez-Knowles, E., Sidhu, K., Dunbier, A. K., Cowens, J. W. et al. Comparison of PAM50 risk of recurrence score with oncotype DX and IHC4 for predicting risk of distant recurrence after endocrine therapy. J Clin Oncol 2013; 31(22): 2783–90.CrossRefGoogle ScholarPubMed
Kelley, R. K. and Venook, A. P. Prognostic and predictive markers in stage II colon cancer: is there a role for gene expression profiling? Clin Colorectal Cancer 2011; 10(2): 73–80.CrossRefGoogle Scholar
Halling, K. C., Schrijver, I. and Persons, D. L. Test verification and validation for molecular diagnostic assays. Arch Pathol Lab Med 2012; 136(1): 11–13.CrossRefGoogle ScholarPubMed
Robertson, K. D. DNA methylation and human disease. Nat Rev Genet 2005; 6(8): 597–610.CrossRefGoogle ScholarPubMed
Bird, A. P. CpG-rich islands and the function of DNA methylation. Nature 1986; 321(6067): 209–13.CrossRefGoogle ScholarPubMed
Herman, J. G. and Baylin, S. B. Gene silencing in cancer in association with promoter hypermethylation. New Engl J Med 2003; 349(21): 2042–54.CrossRefGoogle ScholarPubMed
Baylin, S. B., Herman, J. G., Graff, J. R., Vertino, P. M. and Issa, J. P. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res 1998; 72: 141–96.Google ScholarPubMed
Lander, E. S. The new genomics: global views of biology. Science 1996; 274(5287): 536–9.CrossRefGoogle ScholarPubMed
International HapMap Consortium, A haplotype map of the human genome. Nature 2005; 437(7063): 1299–320.Google Scholar
Kruglyak, L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22(2): 139–44.CrossRefGoogle ScholarPubMed
Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E. and Kutay, U. Nuclear export of microRNA precursors. Science 2004; 303(5654): 95–8.CrossRefGoogle ScholarPubMed
Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136(2): 215–33.CrossRefGoogle ScholarPubMed
Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 2005; 37(7): 766–70.CrossRefGoogle ScholarPubMed
Nelson, P. T., Baldwin, D. A., Scearce, L. M., Oberholtzer, J. C., Tobias, J. W. and Mourelatos, Z. Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 2004; 1(2): 155–61.CrossRefGoogle ScholarPubMed
Esquela-Kerscher, A. and Slack, F. J. Oncomirs – microRNAs with a role in cancer. Nat Rev Cancer 2006; 6(4): 259–69.CrossRefGoogle ScholarPubMed
Volinia, S., Calin, G. A., Liu, C. G., Ambs, S., Cimmino, A., Petrocca, F. et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 2006; 103(7): 2257–61.CrossRefGoogle ScholarPubMed
Si, M. L., Zhu, S., Wu, H., Lu, Z., Wu, F. and Mo, Y. Y. miR-21-mediated tumor growth. Oncogene 2007; 26(19): 2799–803.CrossRefGoogle ScholarPubMed
Taylor, D. D. and Gercel-Taylor, C. MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecol Oncol 2008; 110(1): 13–21.CrossRefGoogle ScholarPubMed
Valadi, H., Ekstrom, K., Bossios, A., Sjostrand, M., Lee, J. J. and Lotvall, J. O. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 2007; 9(6): 654–9.CrossRefGoogle ScholarPubMed
Lawrie, C. H., Gal, S., Dunlop, H. M., Pushkaran, B., Liggins, A. P., Pulford, K. et al. Detection of elevated levels of tumour-associated microRNAs in serum of patients with diffuse large B-cell lymphoma. Br J Haematol 2008; 141(5): 672–5.CrossRefGoogle ScholarPubMed
Boeri, M., Verri, C., Conte, D., Roz, L., Modena, P., Facchinetti, F. et al. MicroRNA signatures in tissues and plasma predict development and prognosis of computed tomography detected lung cancer. Proc Natl Acad Sci USA 2011; 108(9): 3713–18.CrossRefGoogle ScholarPubMed
Gee, H. E., Buffa, F. M., Camps, C., Ramachandran, A., Leek, R., Taylor, M. et al. The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis. Br J Cancer 2011; 104(7): 1168–77.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×