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Genome Wide Profiling of Paired Cancerous and Normal Breast Tissues and Rapid Interpretation of Gene Expression Data

mber of genes differently expressed Table 2. ANOVA Statistical Analysis: number of genes detected by the Applied Biosystems Expression Array System with the corresponding p-value as determined by the Spotfire software application (Sommerville, MA, USA). are differentially expressed (ANOVA p < 0.01). Some known breast cancer genes (for example, BRCA1, erB2, TF2R, etc.) along with a housekeeping gene GAPDH were included.

TaqMan Gene Expression Assays for these genes were ordered through the Applied Biosystems store at http://www.appliedbiosystems.com/ catalog using assay IDs provided in the Oracle Database.

Fold changes were compared for differential gene expression between tumor (primary or metastasis) samples and control (normal) samples, as measured by the Expression Array System and by quantitative real-time PCR using the Applied Biosystems 7900HT Sequence Detection System. Four replicates were performed for each TaqMan Gene Expression Assay and the resultant averaged cycle threshold (CT) was determined. Fold changes for the TaqMan assay were calculated using relative quantitation using GAPDH gene expression and the delta CT method (delta CT = delta CT tumor-delta CTT normal). Expression Array System fold change was determined by calculating the ratio of global normalized signals from primary or metastasis tumor samples to that of their normal tissue sample. The fold change data measured by both platforms correlated very well in both patients, indicating a high degree of concordance between the Applied Biosystems Expression Array System and the TaqMan assay reagents (Figure 5).

Summary

This study examined genome-wide expression profiling of paired cancerous and normal breast tissues using the Applied Biosystems Expression Array System. A comparison of normal and cancerous breast tissue identified statistically significant gene expression change
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