title: Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.
abstract: OBJECTIVE
  Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues.
  
  
  METHODS
  DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability.
  
  
  RESULTS
  The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification.
  
  
  CONCLUSIONS
  Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.
authors.affiliation: 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey;
authors.forename: Burcu
authors.initials: B
authors.lastname: Sengüven
authors.affiliation: 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey;
authors.forename: Emre
authors.initials: E
authors.lastname: Baris
authors.affiliation: 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey;
authors.forename: Tulin
authors.initials: T
authors.lastname: Oygur
authors.affiliation: 2. Pharmacoeconomy and Pharmacoepidemiology Research Center (PEPIRC), Yeditepe University, Istanbul, Turkey.
authors.forename: Mehmet
authors.initials: M
authors.lastname: Berktas
mesh_terms: D002725:Chloroform; D004273:DNA, Neoplasm / Q000235:genetics* / Q000302:isolation & purification*; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding / Q000379:methods
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde; D002725:Chloroform
keywords: DNA extraction; formalin fixed paraffin-embedded tissues.