SHORT REPORT

PCR analysis in archival postmortem tissues

S Bonin¹, F Petrera¹, B Niccolini¹ and G Stanta²

¹ ICGEB, International Centre for Genetic Engineering and Biotechnology, 99 Padriciano, 34012 Trieste, Italy
² Department of Clinical, Morphological and Technological Sciences, University of Trieste, Cattinara Hospital, 447 Strada di Fiume, 34149 Trieste, Italy

Correspondence to:
Correspondence to:
Dr G Stanta, ICGEB, International Centre for Genetic Engineering and Biotechnology, 99 Padriciano, 34012 Trieste, Italy;
stanta{at}icgeb.org

Background: Formalin fixed and paraffin wax embedded tissues of necropsy origin are an important source for molecular analysis especially in rare diseases, neuropathology, or molecular epidemiology studies. Because of DNA degradation, only short sequences can be amplified from this type of tissue, very often less than 100 bases. This poses problems because studies on polymorphism and mutations occurring in large genes often require the analysis of long sequences.

Methods: The development of a simple treatment to obtain longer fragments of DNA for the analysis of archival postmortem paraffin wax embedded tissues.

Results: It was possible to amplify longer sequences ranging up to 300 bases from postmortem tissues, with no modification to the usual DNA extraction procedures. To obtain longer stretches of DNA, a pre-PCR restoration treatment was required, by filling single strand breaks, followed by a vigorous denaturation step.

Conclusions: The development of this simple treatment allowed the analysis of longer fragments of DNA obtained from archival postmortem paraffin wax embedded tissues.

Keywords: formalin fixed paraffin embedded tissues; polymerase chain reaction; DNA degradation; postmortem tissues

Abbreviations: ApoE, apolipoprotein E; PCR, polymerase chain reaction

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

• Harbeck, N., Nimmrich, I., Hartmann, A., Ross, J. S., Cufer, T., Grutzmann, R., Kristiansen, G., Paradiso, A., Hartmann, O., Margossian, A., Martens, J., Schwope, I., Lukas, A., Muller, V., Milde-Langosch, K., Nahrig, J., Foekens, J., Maier, S., Schmitt, M., Lesche, R. (2008). Multicenter Study Using Paraffin-Embedded Tumor Tissue Testing PITX2 DNA Methylation As a Marker for Outcome Prediction in Tamoxifen-Treated, Node-Negative Breast Cancer Patients. JCO 26: 5036-5042 [Abstract] [Full Text]  
• Hata, D. J., Buckwalter, S. P., Pritt, B. S., Roberts, G. D., Wengenack, N. L. (2008). Real-Time PCR Method for Detection of Zygomycetes. J. Clin. Microbiol. 46: 2353-2358 [Abstract] [Full Text]  
• Arias, Y R, Carrillo, E F, Aristizabal, F A (2007). Plasma DNA restoration for PCR applications. J. Clin. Pathol. 60: 952-954 [Full Text]  
• Ghazani, A A, Arneson, N C R, Warren, K, Done, S J (2006). Limited tissue fixation times and whole genomic amplification do not impact array CGH profiles.. J. Clin. Pathol. 59: 311-315 [Abstract] [Full Text]  
• Rosado, M. F., Byrne, G. E. Jr, Ding, F., Fields, K. A., Ruiz, P., Dubovy, S. R., Walker, G. R., Markoe, A., Lossos, I. S. (2006). Ocular adnexal lymphoma: a clinicopathologic study of a large cohort of patients with no evidence for an association with Chlamydia psittaci. Blood 107: 467-472 [Abstract] [Full Text]  
• Bonin, S, Petrera, F, Rosai, J, Stanta, G (2005). DNA and RNA obtained from Bouin's fixed tissues. J. Clin. Pathol. 58: 313-316 [Abstract] [Full Text]  
• O Faolain, E., Hunter, M. B., Byrne, J. M., Kelehan, P., Lambkin, H. A., Byrne, H. J., Lyng, F. M. (2005). Raman Spectroscopic Evaluation of Efficacy of Current Paraffin Wax Section Dewaxing Agents. J. Histochem. Cytochem. 53: 121-129 [Abstract] [Full Text]  
• Gloghini, A., Canal, B., Klein, U., Dal Maso, L., Perin, T., Dalla-Favera, R., Carbone, A. (2004). RT-PCR Analysis of RNA Extracted from Bouin-Fixed and Paraffin-Embedded Lymphoid Tissues. J. Mol. Diagn. 6: 290-296 [Abstract] [Full Text]  
• Zsikla, V, Baumann, M, Cathomas, G (2004). Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR. J. Clin. Pathol. 57: 654-656 [Abstract] [Full Text]