Editing Comparative genomic hybridization (section)

===Methodology===

Array CGH is based on the same principle as conventional CGH. In both techniques, DNA from a reference (or control) sample and DNA from a test (or patient) sample are differentially labelled with two different fluorophores and used as [[hybridization probe|probes]]  that are cohybridized competitively onto [[nucleic acid]] targets. In conventional CGH, the target is a reference metaphase spread. In array CGH, these targets can be genomic fragments cloned in a variety of vectors (such as [[Bacterial artificial chromosome|BACs]] or [[plasmids]]), [[Complementary DNA|cDNAs]], or [[oligonucleotides]].<ref name="Bejjani,Shaffer">Bejjani BA, Shaffer LG (2006) Applications of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 8:528–533.</ref>

Figure 2.<ref name="Oostlander,Meijer,Ylstra" /> is a schematic overview of the array CGH technique. DNA from the sample to be tested is labeled with a red fluorophore ([[Cyanine]] 5) and a reference DNA sample is labeled with green fluorophore (Cyanine 3). Equal quantities of the two DNA samples are mixed and cohybridized to a DNA microarray of several thousand evenly spaced cloned DNA fragments or oligonucleotides, which have been spotted in triplicate on the array. After hybridization, digital imaging systems are used to capture and quantify the relative fluorescence intensities of each of the hybridized fluorophores.<ref name="Bejjani,Shaffer" /> The resulting ratio of the fluorescence intensities is proportional to the ratio of the copy numbers of DNA sequences in the test and reference genomes. If the intensities of the flurochromes are equal on one probe, this region of the patient's genome is interpreted as having equal quantity of DNA in the test and reference samples; if there is an altered Cy3:Cy5 ratio this indicates a loss or a gain of the patient DNA at that specific genomic region.<ref>Shinawi M, Cheung SW (2008) The array CGH and its clinical applications. Drug Discovery Today 13:760–769.</ref>