Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

The development of DNA microarrays can be traced to the late 1990s and early 2000s where methods for fluorescent detection were adapted for the progression of array technology. 23 DNA microarrays can be used for quantification of either genomic DNA or RNA. There are two types of DNA microarray: 2-channel and 1-channel arrays. In 2-channel array, the array slides are made by spotting with cDNA fragments (custom cDNA array) or oligonucleotide probes (Agilent). The treated sample's cDNA and the normal control sample's cDNA are labeled by two types of fluorescence(2-channel). For example, cDNA from tumor samples may be labeled with Cy®5 while cDNA from normal tissue samples may be labeled with Cy®3.The mixture of treated and control samples are then hybridized on array. The ratio of the 2-channel intensities of each spot represents the gene expression of treated sample relative to control. Now Agilent produces commercial 2-channel arrays. 24 , 25 In 1-channel array, the oligonucleotide probes are synthesized on the surface of slide. The fluorescent labeled sample cDNAs are then hybridized on the array and the absolute intensity of hybridization signal is measured. Affymetrix GeneChip is a typical 1-channel array. 24, 26 Illumina BeadArray is a variation of 1-channel array which synthesizes barcoded probes on a surface of microbeads and makes cells filled with beads. 27 A DNA microarray assay needs a commercial array or custom designed array and cDNA labelling preparation from each RNA sample. Following hybridization of the cDNA samples on array, a scanning device images and measures the fluorescent levels of the microarray.