Microarray-based Comparative Genomic Hybridization (Array CGH) is a technique that measures DNA copy number changes and maps them directly onto the genomic sequence. Such copy number aberrations are common in cancer and in many developmental abnormalities.
A microarray for array CGH is assembled by spotting DNA onto a substrate - we use PCR representations of BACs (see Snijders, et. al. in Publications). Next, test and reference DNA (e.g. DNA from a tumor and DNA from a normal genome) are differentially labeled with fluorocromes (e.g. Cy3 and Cy5) and hybridized to the microarray. The normalized fluorescence ratio of the test vs. reference hybridization intensities at each spot on the array indicate the relative copy number at the genomic location mapped to that spot. The resolution of the array is determined by the number of clones in the array, the genomic length of the clones, and the genomic spacing between them.
Following are two papers (PDF format) that explain in more detail the theory and practice of Array CGH:
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