Humana Press, Methods in Molecular Biology, p. 267-278
Array-CGH involves the comparison of a test to a reference genome using a microarray composed of target sequences with known chromosomal coordinates. The test and reference DNA samples are used as templates to generate two probe DNAs labeled with distinct fluorescent dyes. The two probe DNAs are co-hybridized on a microarray in the presence of Cot-1 DNA to suppress unspecific hybridization of repeat sequences. After slide washes and drying, microarray images are acquired on a laser scanner and fluorescent intensities from every target sequence spot on the array are extracted using dedicated computer programs. Intensity ratios are calculated and normalized to enable data interpretation. Although the protocols explained in this chapter correspond primarily to the use of large-insert clone microarrays in either manual or automated fashion, necessary adaptations for hybridization on microarrays composed of shorter target DNA sequences are also briefly described.