Transcriptomics

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Biological Classification of Breast Cancer by Real-Time Quantitative RTPCR: Comparisons to Microarray and Histopathology


ABSTRACT: Microarrays have shown that gene expression patterns can be used to molecularly classify breast cancers into distinct and clinically significant groups. In order to translate these profiles into routine diagnostics, we have recapitulated a microarray breast cancer classification using real-time quantitative (q)RT-PCR. We performed statistical analyses on multiple independent microarray datasets to select an “intrinsic” gene set that can classify breast tumors into four different subtypes designated as Luminal, Normal-like, HER2+/ER-, and Basal-like. A minimal gene set from the microarray “intrinsic” list, and additional genes important for outcome (e.g., proliferation genes), were used to develop a real-time qRT-PCR assay comprised of 53 classifiers and 3 housekeepers. We prospectively compared the expression data and classifications from microarray and real-time qRT-PCR using 123 unique breast samples (117 invasive carcinomas, 1 fibroadenoma and 5 normal tissues) and 3 cells lines. The overall correlation for the 50 genes in common between microarray and qRT-PCR was 0.76. There was 91% (114/126) concordance in the hierarchical clustering classification of the real-time qRT-PCR minimal “intrinsic” gene set (37 genes) and the larger (402 genes) microarray gene set from which the PCR list was derived. As expected, the Luminal tumors (ER+) had a significantly better outcome than the HER2+/ER- (p=0.043) and Basal-like tumors (p=0.001). High expression of the proliferation genes GTBP4 (p=0.011), HSPA14 (p=0.023), and STK6 (p=0.027) were significant predictors of relapse free survival (RFS) independent of grade and stage. Our study shows that genomic microarray data can be translated into a qRT-PCR diagnostic assay that enhances the ability to predict outcome and may therefore improve the standard of care in breast cancer. Keywords: other

ORGANISM(S): Homo sapiens

PROVIDER: GSE2607 | GEO | 2006/01/31

SECONDARY ACCESSION(S): PRJNA92079

REPOSITORIES: GEO

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