Comparative genomic hybridization



Comparative genomic hybridization (CGH) or Chromosomal Microarray Analysis (CMA) is a molecular-cytogenetic method for the analysis of copy number changes (gains /losses) in the DNA content of a given subject's DNA and often in tumor cells. The method is based on the hybridization of fluorescently labeled tumor DNA (frequently fluorescein (FITC)) and normal DNA (frequently rhodamine or Texas Red) to normal human metaphase preparations. Using epifluorescence microscopy and quantitative image analysis, regional differences in the fluorescence ratio of gains/losses vs. control DNA can be detected and used for identifying abnormal regions in the genome. CGH will detect only unbalanced chromosomes changes. Structural chromosome aberrations such as balanced reciprocal translocations or inversions can not be detected, as they do not change the copy number.

DNA from subject tissue and from normal control tissue (reference) is labeled with different colors. After mixing subject 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. Currently, strategically placed Oligos offer a resolution typically of 20-80 base pairs, as compared to the older BAC arrays offering resolution of 100kb. The (fluorescence) color ratio along the chromosomes is used to evaluate regions of DNA gain or loss in the subject sample.

Aside from analyzing cancer cells, the test is valuable at looking for previously unkown mutations that can lead to children with dysmorpahic features, developmental delays, mental retardation, and autism.

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 5-10 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.

Due to the normalization to the most frequent ratio level as "normal", both CGH and array CGH do not provide information as to the ploidy. Since having a balanced DNA content, a tetraploid clone without further rearrangements would appear normal in CGH.