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. 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. Technological approaches to array CGH Array CGH has been implemented using a wide variety of techniques. Therefore, some of the advantages and limitations of array CGH are dependent on the technique chosen. The initial approaches used arrays produced from large insert genomic DNA clones, such as BACs. The use of BACs provides sufficient intense signals to detect single-copy changes and to locate aberration boundaries accurately. However, initial DNA yields of isolated BAC clones are low and DNA amplification techniques are necessary. These techniques include ligation-mediated polymerase chain reaction (PCR), degenerate primer PCR using one or several sets of primers, and rolling circle amplification. Arrays can also be constructed using cDNA. These arrays currently yield a high spatial resolution, but the number of cDNAs is limited by the genes that are encoded on the chromosomes, and their sensitivity is low due to cross-hybridization. This results in the inability to detect single copy changes on a genome wide scale. The latest approach is spotting the arrays with short oligonucleotides. The amount of oligos is almost infinite, and the processing is rapid, cost-effective, and easy. Although oligonucleotides do not have the sensitivity to detect single copy changes, averaging of ratios from oligos that map next to each other on the chromosome can compensate for the reduced sensitivity. It is also possible to use arrays which have overlapping probes so that specific breakpoints may be uncovered. Design approaches There are two approaches to the design of microarrays for CGH applications: whole genome and targeted. Whole genome arrays are designed to cover the entire human genome. They often include clones that provide an extensive coverage across the genome; and arrays that have contiguous coverage, within the limits of the genome. Whole-genome arrays have been constructed mostly