High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil.
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.
Lin
Jianghai
J
Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK.
Kennedy
Stephen H
SH
Svarovsky
Therese
T
Rogers
Jeffrey
J
Kemnitz
Joseph W
JW
Xu
Anlong
A
Zondervan
Krina T
KT
D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D005404:Fixatives / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D008899:Mineral Oil / Q000737:chemistry*; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D013997:Time Factors
D005404:Fixatives; D005557:Formaldehyde; D008899:Mineral Oil; D004247:DNA
Histochem Cell Biol. 2004 Sep;122(3):211-8
15322858
Methods Mol Biol. 2000;132:365-86
10547847
Pathology. 2007 Jun;39(3):345-8
17558863
N Engl J Med. 2005 Mar 10;352(10):997-1003
15758010
Res Vet Sci. 2009 Jun;86(3):421-6
18926550
Neoplasma. 1996;43(2):75-81
8843966
Am J Hum Genet. 2005 Sep;77(3):365-76
16080113
Pathol Res Pract. 2008;204(9):633-6
18573618
PLoS One. 2007 Jun 20;2(6):e537
17579711
Hum Reprod. 2004 Feb;19(2):448-55
14747196
Nucleic Acids Res. 2007;35(12):e85
17576663
Hum Reprod. 2007 Mar;22(3):717-28
17158817