Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

Search BRD Papers

Comparison of methods for extracting DNA from formalin-fixed paraffin sections for nonisotopic PCR.

Author(s): Frank TS, Svoboda-Newman SM, Hsi ED

Publication: Diagn Mol Pathol, 1996, Vol. 5, Page 220-4

PubMed ID: 8866237 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare five methods of DNA extraction using a single archived FFPE tissue specimen for amplification of a 255 bp fragment from the p53 gene using PCR.

   Summary of Findings:

   The authors identified proteinase K digestion overnight (without detergents or EDTA) and sample boiling (as an alternative to phenol-chloroform extraction) as the optimal DNA extraction method for FFPE specimens. DNA extracted by the method above yielded crisp and specific bands with a clean background using a 1:1000 dilution of the extracted DNA sample as template. Other extraction methods required a more concentrated DNA sample, or resulted in nonspecific bands or inhibition of the PCR reaction due to chemical additives during extraction.

   Biospecimens

   • Tissue - Lymph Node

   Preservative Types

   • Formalin

   Diagnoses:

   • Not specified

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	Proteinase K digestion alone Proteinase K with EDTA Proteinase K with EDTA then phenol-chloroform Proteinase K in a sonicating water bath Boiling without dewaxing or proteinase K
   PCR Specific	Template/input amount	1:10 DNA dilution 1:100 DNA dilution 1:1000 DNA dilution 1:10000 DNA dilution

   View more