A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue

Joon Yong Chung, Joo Mi Yi, Ran Xie, Victoria Brown, Olivia Lee, Nita Ahuja, Till Braunschweig, Stephen M. Hewitt

Research output: Contribution to journalArticle

Abstract

As emerging novel DNA-based methodologies are adopted, nucleic acid-based assays depend critically on the quality and quantity of extracted DNA. Formalin-fixed, paraffin embedded (FFPE) tissue samples provide an invaluable resource for subsequent molecular studies of clinical phenotypes, but high-quality DNA extraction from archival FFPE tissue specimens remains complex and time-consuming. To address this challenge, we have developed a reliable rapid DNA extraction method for FFPE tissue specimens. It is based on deparaffinization at high temperature coupled with relieving crosslink in a pressure cooker. The DNA yield by this rapid method resulted in an average 1.8-fold increase in comparison with the commercial kit and OD 260/280 ratios between 1.87 and 1.95. The DNA obtained by the rapid method was suitable for methylation analyses in colon cancer patients. These data suggest that this new DNA extraction method coupled with methylation-specific polymerase chain reaction can be used for epigenetic studies with the advantages of rapidity and high quality and may contribute to the development of biomarkers in clinical studies.

Original languageEnglish (US)
Pages (from-to)128-134
Number of pages7
JournalAnalytical Biochemistry
Volume425
Issue number2
DOIs
StatePublished - Jun 15 2012

Fingerprint

Cooking
Paraffin
Formaldehyde
Tissue
Pressure
DNA
Methylation
Polymerase chain reaction
Biomarkers
Epigenomics
Colonic Neoplasms
Nucleic Acids
Assays
Phenotype
Polymerase Chain Reaction
Temperature

Keywords

  • DNA extraction
  • DNA methylation
  • Formalin-fixed paraffin-embedded tissues
  • Intraepithelial neoplasia
  • Methylation-specific PCR (MSP)

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology
  • Cell Biology

Cite this

A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue. / Chung, Joon Yong; Yi, Joo Mi; Xie, Ran; Brown, Victoria; Lee, Olivia; Ahuja, Nita; Braunschweig, Till; Hewitt, Stephen M.

In: Analytical Biochemistry, Vol. 425, No. 2, 15.06.2012, p. 128-134.

Research output: Contribution to journalArticle

Chung, JY, Yi, JM, Xie, R, Brown, V, Lee, O, Ahuja, N, Braunschweig, T & Hewitt, SM 2012, 'A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue', Analytical Biochemistry, vol. 425, no. 2, pp. 128-134. https://doi.org/10.1016/j.ab.2012.03.012
Chung, Joon Yong ; Yi, Joo Mi ; Xie, Ran ; Brown, Victoria ; Lee, Olivia ; Ahuja, Nita ; Braunschweig, Till ; Hewitt, Stephen M. / A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue. In: Analytical Biochemistry. 2012 ; Vol. 425, No. 2. pp. 128-134.
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