title: Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.
abstract: METHODS
  Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material.
  
  
  RESULTS
  We show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7), significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature) showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature) showed very high concordance with the MammaPrint® results.
  
  
  CONCLUSIONS
  We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research.
authors.affiliation: Divisions of Experimental Therapy, Molecular Biology, Surgical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Lorenza
authors.initials: L
authors.lastname: Mittempergher
authors.forename: Jorma J
authors.initials: JJ
authors.lastname: de Ronde
authors.forename: Marja
authors.initials: M
authors.lastname: Nieuwland
authors.forename: Ron M
authors.initials: RM
authors.lastname: Kerkhoven
authors.forename: Iris
authors.initials: I
authors.lastname: Simon
authors.forename: Emiel J Th
authors.initials: EJ
authors.lastname: Rutgers
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Van't Veer
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D015925:Cryopreservation / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics; D005260:Female; D005557:Formaldehyde / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding / Q000379:methods*; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D005557:Formaldehyde