title: A Critical Evaluation of the PAXgene Tissue Fixation System:  Morphology, Immunohistochemistry, Molecular Biology, and Proteomics.
abstract: OBJECTIVE
  To evaluate the PAXgene tissue fixation system.
  
  
  METHODS
  Clinical biospecimens (n = 46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]).
  
  
  RESULTS
  PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results.
  
  
  CONCLUSIONS
  While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: William
authors.initials: W
authors.lastname: Mathieson
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Marcon
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg.
authors.forename: Laurent
authors.initials: L
authors.lastname: Antunes
authors.affiliation: Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom.
authors.forename: David A
authors.initials: DA
authors.lastname: Ashford
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg.
authors.forename: Fay
authors.initials: F
authors.lastname: Betsou
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg.
authors.forename: Sonia G
authors.initials: SG
authors.lastname: Frasquilho
authors.affiliation: From the Integrated Biobank of Luxembourg, Luxembourg.
authors.forename: Olga A
authors.initials: OA
authors.lastname: Kofanova
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: Siobhan C
authors.initials: SC
authors.lastname: McKay
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: Stephan
authors.initials: S
authors.lastname: Pericleous
authors.affiliation: Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom.
authors.forename: Colleen
authors.initials: C
authors.lastname: Smith
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: Kristian M
authors.initials: KM
authors.lastname: Unger
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: Constanze
authors.initials: C
authors.lastname: Zeller
authors.affiliation: Department of Surgery and Cancer, Imperial College London, London, United Kingdom Wales Cancer Bank, Singleton Hospital, Swansea, United Kingdom. Geraldine.Thomas@imperial.ac.uk.
authors.forename: Geraldine A
authors.initials: GA
authors.lastname: Thomas
mesh_terms: D019342:Acetic Acid; D000328:Adult; D000368:Aged; D002277:Carcinoma / Q000175:diagnosis; D003110:Colonic Neoplasms / Q000175:diagnosis; D000431:Ethanol; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry; D008175:Lung Neoplasms / Q000175:diagnosis; D008297:Male; D000432:Methanol; D008875:Middle Aged; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D040901:Proteomics / Q000379:methods; D055732:Pulmonary Aspergillosis / Q000175:diagnosis; D046888:Tissue Array Analysis; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D000431:Ethanol; D019342:Acetic Acid; D000432:Methanol
keywords: DNA; FFPE; Formalin; Method Validation; PFPE; Protein; RNA; Tissue Microarray