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

Introduction

Microarrays offer a powerful means of studying human gene activity and thereby providing insight into cellular, molecular, and biological changes. Applied Biosystems has developed the Expression Array System, a complete system for gene expression studies. It includes Human Genome Survey Microarrays (utilizing fully curated transcript data for array design), the 1700 Chemiluminescent Microarray Analyzer, high-sensitivity chemistries optimized for chemiluminescence detection, and full system software including an Oracle Database that contains the most complete and current gene annotation. This integrated system not only offers a significant performance improvement over existing microarray technologies, but can be linked to the Celera Discovery System and TaqMan Gene Expression Assays for further in-depth gene expression analysis. The result is an integrated workflow for unambiguous determination of differential gene expression in various populations, tissues, stages of development, and diseases.

In this application note, we report on the profiling of ~28,000 human genes in paired normal and cancerous breast tissues using the Applied Biosystems Expression Array System. Differentially expressed genes in normal tissue, primary tumor, and metastasis tumor samples were identified by comparing breast tissue specimens from two patients. Additionally, microarray data was validated using quantitative realtime PCR (using TaqMan Gene Expression Assays).

Methods and Materials

This experiment was designed to study gene expression profiling for two patients with three different tissues (normal, primary tumor, and metastasis tumor) using two replicates for each sample (Figure 1). Total RNA samples (from Biochain Inc., Hayward, CA) obtained from two patients were processed into digoxigenin (DIG) -labeled cRNA using the Applied Biosystems Chemilumin
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