title: A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue.
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.
authors.affiliation: Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Joon-Yong
authors.initials: JY
authors.lastname: Chung
authors.forename: Joo Mi
authors.initials: JM
authors.lastname: Yi
authors.forename: Ran
authors.initials: R
authors.lastname: Xie
authors.forename: Victoria
authors.initials: V
authors.lastname: Brown
authors.forename: Olivia
authors.initials: O
authors.lastname: Lee
authors.forename: Nita
authors.initials: N
authors.lastname: Ahuja
authors.forename: Till
authors.initials: T
authors.lastname: Braunschweig
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Hewitt
mesh_terms: D015415:Biomarkers / Q000378:metabolism; D003110:Colonic Neoplasms / Q000378:metabolism / Q000473:pathology; D004247:DNA / Q000032:analysis* / Q000302:isolation & purification; D019175:DNA Methylation; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D045325:HCT116 Cells; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D011312:Pressure; D013696:Temperature; D000094742:Secreted Frizzled-Related Proteins
chemical_list: D015415:Biomarkers; D004247:DNA; D006023:Glycoproteins; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; C117636:SFRP1 protein, human; D000094742:Secreted Frizzled-Related Proteins; C021240:tissue-factor-pathway inhibitor 2