title: Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens.
abstract: BACKGROUND
  Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen.
  
  
  METHODS
  Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol.
  
  
  RESULTS
  All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA.
  
  
  CONCLUSIONS
  These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells.
authors.affiliation: Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India.
authors.forename: Souvik
authors.initials: S
authors.lastname: Ghatak
authors.affiliation: Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India.
authors.forename: Zothan
authors.initials: Z
authors.lastname: Sanga
authors.affiliation: Mizoram State Cancer Institute, Zemabawk, Aizawl, Mizoram, India.
authors.forename: Jeremy L
authors.initials: JL
authors.lastname: Pautu
authors.affiliation: Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India.
authors.forename: Nachimuthu Senthil
authors.initials: NS
authors.lastname: Kumar
mesh_terms: D000328:Adult; D004247:DNA / Q000032:analysis* / Q000235:genetics; D020869:Gene Expression Profiling; D050259:Genes, Mitochondrial; D005814:Genes, Viral; D006801:Humans; D008875:Middle Aged; D009367:Neoplasm Staging; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D012313:RNA / Q000032:analysis* / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013274:Stomach Neoplasms / Q000188:drug therapy* / Q000473:pathology; D016707:Tissue Fixation
chemical_list: D012333:RNA, Messenger; D012313:RNA; D004247:DNA
keywords: Helicobacter pylori; PCR diagnosis; archived samples; mitochondrial DNA; nucleic acid co-extraction; reverse transcription