Comparative genomic hybridization
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Comparative genomic hybridization (CGH) is a molecular-cytogenetic method for the analysis of copy number changes (gains /losses) in the DNA content of tumor cells. The method is based on the hybridization of fluorescently labeled tumor (frequently Fluorescein - FITC) and normal DNA (frequently Rhodamine or Texas Red) to normal human metaphase preparations. Using epiflourescence microscopy and quantitative image analysis, regional differences in the fluorescence ratio of tumor vs. control DNA can be detected and used for identifying abnormal regions in the tumor cell genome. CGH will detect only unbalanced chromosomes changes. Structural chromosome aberrations such as balanced reciprocal translocations, inversions can not be detected.
DNA from tumor tissue and from normal control tissue (reference) is labeled with different colors. After mixing tumor and reference DNA along with unlabeled human cot 1 DNA to suppress repetitive DNA sequences, the mix is hybridized to normal metaphase chromosomes or, for array- or matrix-CGH, to a slide containing hundreds or thousands of defined DNA probes. The (fluorescence) color ratio along the chromosomes is used to evaluate regions of DNA gain or loss in the tumor sample.
[edit] Technical considerations
CGH is capable of detecting loss, gain and amplification of the copy number at the levels of chromosomes. However, by current (2006) standards, it is considered that to detect a single copy loss, the region must be at least 10 Mb in length. On the other hand, detection of amplification is known to be sensitive down to less than 1 Mb. Therefore, one must take into consideration that while CGH is sensitive to amplification, it is an order of magnitude less sensitive to loss.
The use of array CGH overcomes many of these limitations, with improvement in resolution and dynamic range, in addition to direct mapping of aberrations to the genome sequence and improved throughput.
It is essential to note that that both CGH and array CGH do not provide information as to the ploidy or location of the rearranged sequences.
[edit] See also
Array based Comparative Genomic Hybridization
[edit] External links
- Progenetix database: A large collection of CGH data from publications (> 13000 cases, 2006).
- CGHtracker: An attempt to list all CGH publications containing original case data. This is part of the Progenetix project.
- NCBI's Cancer Chromosomes: Cancer Chromosome is an integral part of NCBI's Entrez system, which combines several databases that are derived from CGH data.
