Limitations
Chromosomal CGH is capable of detecting loss, gain and amplification of the copy number at the levels of chromosomes. However, it is considered that to detect a single copy loss the region must be at least 5–10 Mb in length. Detection of amplifications (e.g. tens or hundreds of copies of one or few neighboring genes) is known to be sensitive down to less than 1 Mb. Therefore, one must take into consideration that while CGH is sensitive to specific types of copy number gains, the resolution of regional deletions is more limited.
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.
Read more about this topic: Comparative Genomic Hybridization
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