Parallel Analysis of Gene Copy Number and Expression Using cDNA Microarrays
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A cDNA microarray consists of hundreds or thousands of polymerase chain reaction (PCR)-amplified cDNAs spotted onto a glass microscope slide, in a high-density pattern of rows and columns (1 ). cDNA microarrays were first used widely to quantify gene expression across hundreds or thousands of genes simultaneously (2 ,3 ). To measure gene expression, mRNAs from two different samples are differentially fluorescently labeled and cohybridized to a cDNA microarray, which is then scanned in dual wavelengths (Fig. 1 A ). For each cDNA element on the microarray, the ratio of fluorescence intensities reflects the relative abundance for that mRNA between the two samples. cDNA microarrays have been utilized to profile gene expression in a variety of organisms (1 ,3 –6 ). In humans, cDNA microarrays have been used extensively to characterize gene expression in cancer, in which patterns of gene expression reveal the molecular phenotypes of tumor cells (7 –9 ).
Fig. 1. Parallel analysis of gene expression and copy number using cDNA microarrays. (A ) Measuring mRNA levels with cDNA microarrays. mRNAs from two different samples (normal and tumor shown) were differentially fluorescently labeled with Cy3 and Cy5, respectively, and cohybridized to a cDNA microarray, which was then scanned in dual wavelengths. For each cDNA element on the microarray, the ratio of fluorescence intensities reflects the relative abundance for that mRNA between the two samples. The ErbB2 gene is depicted as more highly expressed in the tumor sample. (B ) Measuring gene copy number with cDNA microarrays. In this array CGH technique, genomic DNA from two different samples (normal and tumor shown) were differentially fluorescently labeled and cohybridized to a cDNA microarray. For each cDNA element on the microarray, the ratio of fluorescence intensities reflects the relative gene copy number (i.e., amplification or deletion) between the two samples. The ErbB2 gene is depicted as amplified in the tumor sample.
