title: Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue.
abstract: BACKGROUND
  Expression profiling by microarrays and real-time polymerase chain reaction-based assays is a powerful tool for classification and prognostication of disease; however, it remains a research tool, largely reliant on frozen tissue. Limiting the utility of expression profiling is the isolation of quality nucleic acids from formalin-fixed, paraffin-embedded tissue. The collection, handling, and processing of tissue directly impacts the biomolecules that can be recovered from it. High-quality nucleic acids can be obtained from formalin-fixed, paraffin-embedded tissue, but greater attention to all steps in the process of tissue handling and preparation is required.
  
  
  OBJECTIVE
  To summarize the current state-of-the-art of preanalytic factors in tissue handling and processing as they impact the quality of RNA obtainable from formalin-fixed, paraffin-embedded tissue. The goals are to provide recommendations that will improve RNA quality for expression profiling from formalin-fixed, paraffin-embedded tissue and highlight areas for additional research. Tissue is an analyte and it must be handled in a standardized fashion to provide consistent results.
  
  
  METHODS
  The literature was reviewed. Consultation with industry and academic leaders in the use of RNA for expression profiling was obtained to identify areas for additional research.
  
  
  CONCLUSIONS
  Development of RNA-based assays from formalin-fixed, paraffin-embedded tissue is feasible. Greater attention to tissue handling and processing is essential to improve the quality of biospecimens for the development of robust RNA-based assays. Standardization of procedures and vigorous testing of alternative protocols are required to ensure that these assays function as designed.
authors.affiliation: Tissue Array Research Program, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA. genejock@helix.nih.gov
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Hewitt
authors.forename: Fraser A
authors.initials: FA
authors.lastname: Lewis
authors.forename: Yanxiang
authors.initials: Y
authors.lastname: Cao
authors.forename: Richard C
authors.initials: RC
authors.lastname: Conrad
authors.forename: Maureen
authors.initials: M
authors.lastname: Cronin
authors.forename: Kathleen D
authors.initials: KD
authors.lastname: Danenberg
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Goralski
authors.forename: John P
authors.initials: JP
authors.lastname: Langmore
authors.forename: Rajiv G
authors.initials: RG
authors.lastname: Raja
authors.forename: P Mickey
authors.initials: PM
authors.lastname: Williams
authors.forename: John F
authors.initials: JF
authors.lastname: Palma
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
mesh_terms: D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods; D016591:Histocytological Preparation Techniques / Q000379:methods; D006801:Humans; D009696:Nucleic Acids / Q000032:analysis*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016612:Paraffin Embedding; D010340:Pathology, Surgical / Q000379:methods*; D012313:RNA / Q000032:analysis; D013048:Specimen Handling / Q000379:methods
chemical_list: D009696:Nucleic Acids; D005557:Formaldehyde; D012313:RNA