title: Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA 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. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens.
  
  
  RESULTS
  For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and -RNA than the two other methods, and particularly provides higher quality microRNAs and genomic DNA for subsequent molecular analyses.
  
  
  CONCLUSIONS
  We determined that co-extraction of genomic DNA and total RNA from a single FFPE specimen is an effective recovery approach to obtain high-quality material for parallel molecular and high-throughput analyses. Our optimized approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies.
authors.affiliation: Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America.
authors.forename: Adam
authors.initials: A
authors.lastname: Kotorashvili
authors.forename: Andrew
authors.initials: A
authors.lastname: Ramnauth
authors.forename: Christina
authors.initials: C
authors.lastname: Liu
authors.forename: Juan
authors.initials: J
authors.lastname: Lin
authors.forename: Kenny
authors.initials: K
authors.lastname: Ye
authors.forename: Ryung
authors.initials: R
authors.lastname: Kim
authors.forename: Rachel
authors.initials: R
authors.lastname: Hazan
authors.forename: Thomas
authors.initials: T
authors.lastname: Rohan
authors.forename: Susan
authors.initials: S
authors.lastname: Fineberg
authors.forename: Olivier
authors.initials: O
authors.lastname: Loudig
mesh_terms: D000293:Adolescent; D000328:Adult; D000818:Animals; D002648:Child; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification*; D005260:Female; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D066298:In Vitro Techniques; D051379:Mice; D035683:MicroRNAs / Q000032:analysis*; D016612:Paraffin Embedding / Q000379:methods*; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification*; D012333:RNA, Messenger / Q000032:analysis*; D016707:Tissue Fixation / Q000379:methods*; D055815:Young Adult
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D005557:Formaldehyde; D012313:RNA; D004247:DNA