title: A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?
abstract: BACKGROUND
  Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses.
  
  
  OBJECTIVE
  To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints.
  
  
  METHODS
  We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints.
  
  
  CONCLUSIONS
  Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.
authors.affiliation: From the Kelly Government Solutions Program, Kelly Services, Rockville (Drs Bass and Greytak), and the Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda (Dr Moore), Maryland; and the Preferred Solutions Group, Arlington, Virginia (Dr Engel).
authors.forename: B Paige
authors.initials: BP
authors.lastname: Bass
authors.forename: Kelly B
authors.initials: KB
authors.lastname: Engel
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Greytak
authors.forename: Helen M
authors.initials: HM
authors.lastname: Moore
mesh_terms: D004247:DNA / Q000032:analysis; D005404:Fixatives; D005557:Formaldehyde; D006801:Humans; D016612:Paraffin Embedding / Q000379:methods*; D011506:Proteins / Q000032:analysis; D040901:Proteomics; D012313:RNA / Q000032:analysis; D013048:Specimen Handling / Q000379:methods; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D005404:Fixatives; D011506:Proteins; D005557:Formaldehyde; D012313:RNA; D004247:DNA