High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil

Anal Biochem. 2009 Dec 15;395(2):265-7. doi: 10.1016/j.ab.2009.08.016. Epub 2009 Aug 19.

Abstract

Extracting DNA from formalin-fixed and paraffin-embedded (FFPE) tissue remains a challenge, despite numerous attempts to develop a more effective method. Polymerase chain reaction (PCR) success rates with DNA extracted using current methods remain low. We extracted DNA from 140 long-term archived FFPE samples using a simple but effective deparaffinization method, removing the wax with mineral oil, and a commercially available DNA extraction kit. DNA quality was subsequently tested in a genotyping experiment with 14 microsatellite markers. High-quality DNA was obtained with a mean PCR success rate of 97% (range: 88-100%) across markers. The results suggested that DNA extracted using this novel method is likely to be suitable for genetic studies involving DNA fragments <200 bp.

Publication types

  • Technical Report

MeSH terms

  • DNA / chemistry
  • DNA / isolation & purification*
  • Fixatives / chemistry*
  • Formaldehyde / chemistry*
  • Mineral Oil / chemistry*
  • Paraffin Embedding*
  • Polymerase Chain Reaction
  • Time Factors

Substances

  • Fixatives
  • Formaldehyde
  • Mineral Oil
  • DNA