Comparative genome hybridization (CGH) is a molecular cytogenetic method of screening a DNA sample for genetic changes. Originally, the method was based on the differential hybridization of fluorescently labeled DNA from diseased and healthy samples to normal human metaphase preparations [1]. The changes observed are classified as DNA gains and losses and reveal a characteristic pattern that includes mutations and deletions at chromosomal and sub-chromosomal levels [1b and 1c].

In contrast to conventional methods, array-based CGH combines the principle of genomic hybridization with the resolution and sensitivity of high-density DNA microarray technology. It therefore becomes possible for the first time to detect genetic alterations not only at the chromosomal level but at the level of the DNA itself [2]. High-density CGH-arrays therefore pave the way for the identification of disease-related genetic aberrations that have not yet been detected by existing technologies, and array-based CGH technology is applicable for the diagnosis of cancer or genetic diseases in the clinical setting today.