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