Comparative Genomic Hybridization

The key measurement is the relative fluorescence produced by patient and reference DNA after they hybridize to the same genomic targets. When the patient sample contains more or less DNA from a region than the reference, the fluorescence balance shifts at that location. Researchers use these regional differences to identify genomic gains, losses, or amplifications.

Chromosome-based CGH evaluates fluorescence differences across normal chromosomes, whereas array-based CGH measures hybridization across DNA features distributed on a microarray. This array format supports more detailed examination of genomic regions and can reveal submicroscopic deletions and duplications that chromosome-based analysis may not resolve. The choice therefore affects the scale of detectable abnormalities.

Reference DNA provides the comparison needed to interpret the patient sample's genomic representation. Both labeled samples are mixed before hybridization, so fluorescence differences reflect unequal representation between them rather than an isolated signal from the patient alone. This comparative design allows gains, losses, and amplifications to be located across the genome.

A typical workflow begins with patient and reference DNA, followed by fluorescent labeling of the two samples. The labeled material is mixed and hybridized either to normal chromosomes or to a DNA microarray. Researchers then examine regional fluorescence differences to identify genomic areas where the patient and reference samples are not equally represented.

CGH is useful when investigators need to characterize chromosomal abnormalities associated with genetic disease. Its applications include evaluating developmental disorders, unexplained congenital conditions, and genomic changes linked to cancer. By showing where copy-number differences occur, the technique supports both diagnostic investigation and further characterization of the underlying chromosomal abnormality.

The method can identify genomic gains, losses, and amplifications, including submicroscopic deletions and duplications when an array is used. These findings help describe chromosomal abnormalities at a level relevant to genetic disease, cancer-associated genomic changes, developmental disorders, and congenital conditions. The resulting copy-number profile provides information for diagnosis and genomic characterization.