Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.

Author(s): Mittempergher L, de Ronde JJ, Nieuwland M, Kerkhoven RM, Simon I, Rutgers EJ, Wessels LF, Van't Veer LJ

Publication: PLoS One, 2011, Vol. 6, Page e17163

PubMed ID: 21347257 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare gene expression in FFPE and frozen breast specimens by DASL.

   Summary of Findings:

   Hybridization and average signal intensity was lower in FFPE specimens than frozen tissues (p<0.001). There were 11883 probes hybridized in all of the FFPE samples. 94% of these overlapped with the 13370 probes hybridized in all frozen specimens. Cell cycle gene probes that hybridized were enriched in FFPE tissue and RNA processing, DNA repair and transport probes were underrepresented. FFPE technical replicates showed a correlation of 0.95, and the correlation between different specimens was 0.91. In contrast, the correlation for technical replicates of frozen specimens was 0.99. After median recentering, FFPE and the matched frozen specimens grouped together, along with their technical replicates, with a correlation of 0.65-0.89 considering all probes. In contrast, the correlation between non-matched pair FFPE and frozen specimens was 0.002-0.83. In FFPE tissue, the correlations of ER-alpha, PR, and HER2 expression with IHC staining results were 0.71 (p<0.01), 0.89 (p<0.01) and 0.57-0.82 (p<0.01), respectively. When FFPE gene expression data was classified by the single sample predictor or genomic grade index, 19 of 20 FFPE specimens agreed with the frozen counterpart. Using a 60 gene index derivative of the 70 gene prognosis signature, there was a correlation of 0.94 between matched frozen and FFPE specimens, and both specimen types correlated highly with the MammaPrint Indices (>0.88). The probes for which there was the highest correlation between FFPE and frozen specimens were GC rich.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DASL
   Protein	Immunohistochemistry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen
   Immunohistochemistry Specific	Targeted peptide/protein	Estrogen receptor alpha Progesterone receptor HER2
   DASL Specific	Technology platform	Immunohistochemistry

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