Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform.

Author(s): Abramovitz M, Barwick BG, Willis S, Young B, Catzavelos C, Li Z, Kodani M, Tang W, Bouzyk M, Moreno CS, Leyland-Jones B

Publication: Br J Cancer, 2011, Vol. 105, Page 1574-81

PubMed ID: 22067903 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared gene expression data generated using two different DASL panels and compared the data with the breast cancer subtype as defined by pathology IHC in 87 FFPE specimens of invasive carcinoma.  RNA was extracted using High Pure FFPE RNA Micro Kit from three 5µm sections of FFPE blocks that had been stored for 2-3 years. RNA was quantified by spectrophotometer and by real-time PCR amplification of RPL13a. Expression was determined using a custom 512 gene DASL panel as well as Illumina’s human cancer panel. Gene expression was then compared to previously determined IHC results for ER, PR, and HER2. ER and PR IHC staining were classified as negative (<1%) or positive (≥1%). Specimens were considered HER2 positive when IHC staining was scored as 3+ using the ASCO/CAP guidelines or 2+ if amplification was observed by fluorescent in situ hybridization (FISH). Additionally, the authors compared the expression of 30 genes identified in this study to that in publicly available expression data from 295 patients in the Netherlands Cancer Institute and 177 patients from the University of North Carolina Chapel Hill.

   Summary of Findings:

   Gene expression was very strongly correlated between replicate RNA specimens from the same tumor using either the custom breast cancer panel (r²=0.9612) or Illumina’s standard human cancer panel (r²=0.9613). Further, expression levels of the 152 genes included in both panels were strongly correlated (r²=0.88). As expected, tumors that were ER positive by IHC had an average of 4.46-fold higher expression of ESR1 (P=1.1 x 10^-14), tumors that were PR positive by IHC had an average of 3.41-fold higher expression of PGR (P=2.5 x 10^-7) and tumors that were HER2 positive had an average of 3.59-fold higher expression of ERBB2 (P=1.6 x 10^-6). Further, among HER2 positive specimens, ERBB2 expression was highest in specimens that were ER and PR negative. Based on hierarchical clustering, thirty genes were identified that were predictive of cancer subtype but only 10 were included in the Illumina human cancer panel. When this 30 gene expression panel was applied to publicly available data from 177 patients from the University of North Carolina Chapel Hill, it was able to correctly separate the tumors based on subtype. Further, expression of some genes in the 30 gene panel was significantly different by univariate Cox regression analysis among the breast cancer subtypes in both the Netherlands Cancer Institute (295 patients) and University of North Carolina Chapel Hill data sets.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   Protein	Immunohistochemistry
   RNA	DASL

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   DASL Specific	Technology platform	Custom breast cancer panel IHC Standard cancer panel
   Immunohistochemistry Specific	Targeted peptide/protein	HER2 ER PR
   DASL Specific	Targeted nucleic acid	ESR1 PGR ERBB2

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