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Increasing PCR Sensitivity for Amplification from Paraffin-Embedded Tissues

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PCR Cloning Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 192))

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Abstract

Many common molecular biology techniques including polymerase chain reaction (PCR) (1), Southern blotting (2), comparative genomic hybridization (3), and in situ hybridization (4) have been adapted for use with paraffin-embedded tissue (PET). PCR-amplified products from PET can be used for, among others, the analysis of loss of heterozygosity (1), gene amplification (5), direct sequencing, cloning, and characterization of genes (6).

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References

  1. Akalu, A., Elmajian D. A., Highshaw, R. A., Nichols, P. W., and Reichardt, J. K.V. (1999) Somatic mutations at the SRD5A2 locus encoding prostatic steroid 5α-reductase during prostatic cancer progression. J. Urol. 161, 1355–1358.

    Article  CAS  PubMed  Google Scholar 

  2. Bramwell, N. H. and Burns, 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. 116, 730–732.

    Google Scholar 

  3. Speicher, M. R., Jauch, A., Walt, H., du Manoir, S., Schrock, E., Holtgreve-Grez, H., Schoell, C., Lengauer, C., Cremer, T., and Reid, T. (1993) Molecular cytogenic analysis of formalin-fixed, paraffin embedded solid tumors by comparative genomic hybridization. Hum. Mol. Genet. 2, 1907–1914.

    Article  CAS  PubMed  Google Scholar 

  4. Nuovo, G. J. and Silverstein, S. J. (1988) Methods in laboratory investigation: comparison of formalin, buffered formalin, and Bouin’s fixation on the detection of human papillomavirus deoxyribonucleic acid from genital lesions. Lab. Invest. 59, 720–724.

    CAS  PubMed  Google Scholar 

  5. Ribot, E. M., Quinn, F. D., Bai, X., and Murtagh, J. J., Jr. (1998) Comparative PCR: An improved method to detect gene amplification. BioTechniques 24, 22–26.

    Google Scholar 

  6. Crisan, D. and Mattson, J. C. (1993) retrospective DNA analysis using fixed tissue specimens. DNA Cell Biol. 12, 455–464.

    Article  CAS  PubMed  Google Scholar 

  7. Jacson, V. (1978) Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell 15, 945–954.

    Article  Google Scholar 

  8. Zhuang, Z., Bertheau, P., Emmert-Buck, M. R., Liotta, L. A., Gnarra, J., Linehan, W. M., and Lubensky, I. A. (1995) A microdissection technique for archival DNA analysis of specific cell populations in lesions<1 mm in size. Am. J. Pathol. 146, 620–625.

    Google Scholar 

  9. Greer, C. E., Peterson, S. L., Kiviat, N. B., and Manos, M. M. (1991) PCR amplification from paraffin-embedded tissues. Effects of fixative and fixation time. Am. J. Clin. Pathol. 95, 117–124.

    CAS  PubMed  Google Scholar 

  10. Burton, M. P., Schneider, B. G., Brown, R., Escamilla-Ponce, N., and Gulley, M. L. (1997) Comparison of histologic stains for use in PCR analysis of microdissected, paraffinembedded tissues. BioTechniques 24, 86–92.

    Google Scholar 

  11. 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., and Sninsky, J. J., eds.) Academic, San Diego, CA, pp. 32–38.

    Google Scholar 

  12. Akalu, A. and Reichardt, J. K. V. (1999) A reliable PCR amplification method for microdissected cells obtained from paraffin-embedded tissue. Genet. Analyt. 15, 229–233.

    CAS  Google Scholar 

  13. Walch, A., Komminoth, P., Hutzler, P., Aubele, M., Hofler, H., and Werner, M. (2000) Microdissection of tissue section: application to the molecular genetic characterization of premalignant lesions. Pathology 68, 9–17.

    CAS  Google Scholar 

  14. Baisse, B., Bian, Y.-S., and Benhattar, J. (2000) Microdissection by exclusion and DNA extraction for multiple PCR analyses from archival tissue sections. BioTechniques 28, 856–862.

    CAS  PubMed  Google Scholar 

  15. Shimizu, R. and Burns, J. C. (1995) Extraction of nucleic acids: sample preparation from paraffin-embedded tissues, in PCR Strategies (Innis, M. A., Gelfand, D. H., and Sninsky, J. J., White T. J., eds.), Academic, San Diego, CA, pp. 153–136.

    Google Scholar 

  16. Benz-Ezra, J., Johnson, A., Rossi, J., Cook, N., and Wu, A. (1991) Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J. Histochem. Cytochem. 39, 351–354.

    Google Scholar 

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© 2002 Humana Press Inc.

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Akalu, A., Reichardt, J.K.V. (2002). Increasing PCR Sensitivity for Amplification from Paraffin-Embedded Tissues. In: Chen, BY., Janes, H.W. (eds) PCR Cloning Protocols. Methods in Molecular Biology™, vol 192. Humana Press. https://doi.org/10.1385/1-59259-177-9:067

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  • DOI: https://doi.org/10.1385/1-59259-177-9:067

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-969-8

  • Online ISBN: 978-1-59259-177-0

  • eBook Packages: Springer Protocols

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