Abstract
One of the greatest potentials of polymerase chain reaction (PCR) lies in the fact that even minute amounts of target DNA or extensively damaged DNA can be successfully amplified in vitro and thus become amenable to further study. This enables a detailed molecular analysis of small amounts of DNA from tissue that has been damaged by fixation (e.g., in formalin) and long-term storage in paraffin. The applications of this methodology are nearly unlimited. For example, rare tumors that are stored as formalin-fixed, paraffin-embedded tissue in pathology departments throughout the world can be analyzed at the molecular level. Furthermore, tissue from small lesions (e.g., primary skin melanomas), which are only rarely available for molecular analysis since the entire specimen is usually needed for histopathological assessment, can be examined. For PCR analysis, only several sections from the paraffin block, which are usually dispensable, are sufficient. Even small amounts of very low quality DNA can be used, as the sensitivity of the detection of specific target DNA sequences is several orders of magnitude higher than that with any conventional method. For example, Southern blot analysis of DNA from paraffin-embedded tissue has been performed, but with limited success as only relatively small amounts of degraded and irreversibly modified DNA can be obtained from embedded specimens (1,2). Thus, PCR methodology creates an ideal link between traditional histology and modern molecular biology (3).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dubeau, L., Chandler, L. A., Gralow, I. R., Nichols, P. W., and Jones, P. A. (1986) Southern blot analysis of DNA extracted from formalin-fixed pathology specimens. Cancer Res. 46, 2964–2969.
Goelz, S. E., Hamilton, S. R., and Vogelstein, B. (1985) Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem. Biophys. Res. Commun. 130, 118–126.
Shibata, D., Martin, W. J., and Arnheim, N. (1988) Analysis of DNA sequences in forty-year-old paraffin-embedded thin-tissue sections: a bridge between molecular biology and classical histology. Cancer Res. 48, 4564–4566.
Volkennandt, M., McNutt, N. S., and Albino, A. P. (1991) Sequence analysis of DNA from formalin-fixed paraffin-embedded human malignant melanoma. J. Cutaneous Pathol. 18, 210–214.
Wright, D. K. and Manos, M. M. (1990) Sample preparation from paraffin-embedded tissues, in PCR Protocols: A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T. J., eds.), Academic, New York, pp. 153–158.
Kwok, S. and Higuchi, R. (1989) Avoiding false positives with PCR. Nature 339, 237,238.
Ting, Y. and Manos, M. M. (1990) Detection and typing of genital human papillomaviruses, in PCR Protocols: A Guide to Methods and Applications (Innis, M. A., Gelfand, D. H., Sninsky, J. J. and White, T. J., eds.), Academic, New York, pp. 356–361.
Parker, J. D. and Burmer, G. C. (1991) The oligomer extension ‘hot blot’: A rapid alternative to Southern blots for analyzing polymerase chain reaction products. BioTechniques 10, 94–101.
Wu, A. M., Ben Ezra, J., Winberg, C., Colombero, A. M., and Rappaport, H. (1990) Analysis of antigen receptor gene rearrangements in ethanol and formaldehyde-fixed, paraffin-embedded specimens. Lab. Invest. 63, 107–114.
Bramwell, N. H. and Bums, B. F. (1988) The effects of fixative type and fixation time on the quantity and quality of extractable DNA for hybridization studies on lymphoid tissue. Exp. Hematol. 16, 730–732.
Jackson, D. P., Lewis, F. A., Taylor, G. R., Boylston, A. W., and Quirke, P. (1990) Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction. J. Clin. Pathol. 43, 499–504.
Crisan, D. and Mattson, J. C. (1991) PCR amplification of intermediate size DNA sequences from formalin and B-5 fixed bone marrow specimens. Proceedings of the 1991 Miami Bio/Technology Winter Symposium 92 (Abstract).
Herbert, D. J., Nishiyama, R. H., Bagwell, C. B., Munson, M. E., Hitchcox, S. A., and Lovett, E. J., III (1989) Effects of several commonly used fixatives on DNA and total nuclear protein analysis by flow cytometry. Am. J. Clin. Pathol, 91, 535–541.
Rogers, B. B., Alpert, L. C., Hine, E. A., and Buffone, G. J. (1990) Analysis of DNA in fresh and fixed tissue by the polymerase chain reaction. Am. J. Pathol. 136, 541–548.
Weizsacker, F., Labeit, S., Koch, H. K., Oehlert, W., Gerok, W., and Blum, H. E. (1991) A simple and rapid method for the detection of RNA in formalin-fixed, paraffin-embedded tissues by PCR amplification. Bioch. Biophys. Res. Comm. 174, 176–180.
Lampertico, P., Malter, J. S., Colombo, M., and Gerber, M. A. (1990) Detection of hepatitis B virus DNA in formalin-faed, paraffin-embedded liver tissue by the polymerase chain reaction. Am. J. Pathol. 137, 253–258.
Shibata, D. K., Arnheim, N., and Martin, W. J. (1988) Detection of human papilloma virus in paraffin-embedded tissue using the polymerase chain reaction. J. Exp. Med. 167, 225–230.
Higuchi, R. (1990) Rapid, efficient DNA extraction for PCR from cells of blood. Amplifications. A Forum for PCR Users. (May 1989), 1–3.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1993 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Volkenandt, M., Dicker, A.P., Fanin, R., Banerjee, D., Albino, A., Bertino, J.R. (1993). Polymerase Chain Reaction Analysis of DNA from Paraffin-Embedded Tissue. In: White, B.A. (eds) PCR Protocols. Methods in Molecular Biology, vol 15. Humana Press, Totowa, NJ. https://doi.org/10.1385/0-89603-244-2:81
Download citation
DOI: https://doi.org/10.1385/0-89603-244-2:81
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-244-6
Online ISBN: 978-1-59259-502-0
eBook Packages: Springer Protocols