Cytogenetics is a branch of genetics that is concerned with the structural and functional studies of the cell, especially the chromosomes. Cytogenetics is the study of genetic phenomena through the cytological analysis of chromosomes under the light or electron microscope.

It includes routine analysis of G-banded chromosomes, other cytogenetic banding techniques, as well as molecular cytogenetics such as fluorescent in situ hybridization (FISH), multicolour FISH, locus-specific FISH and comparative genomic hybridization (CGH).

I. Chromosome banding

Different staining methods can be utilised to identify individual chromosomes:

1. G (Giemsa) banding: This is the most commonly used method. The chromosomes are treated with trypsin to denature their protein content and then stained with a DNA binding dye known as Giemsa which gives each chromosome a characteristic and reproducible pattern of light and dark bands .
2. Q (Quinacrine) banding: This gives a banding pattern similar to that obtained with Giemsa and requires examination of the chromosome with an ultraviolet fluorescent microscope.
3. R (Reverse) banding: In this technique, the chromosomes are heat denatured before staining with Giemsa, yielding light and dark bands patterns which are reverse of those obtained using conventional G banding .
4. C (Centromeric heterochromatin) banding: In C banding the chromosomes are pretreated with acid prior to G banding, the centromeres and other heterochromatic regions containing highly repetitive DNA are preferentially stained.

II. FISH

Fluorescent in situ hybridization (FISH) is a process that vividly paints chromosomes or portions of chromosomes with fluorescent molecules to identify chromosomal abnormalities (e.g., insertions, deletions, translocations, and amplifications). FISH is commonly used to identify specific chromosomal deletions associated with pediatric syndromes such as DiGeorge syndrome (a deletion of part of chromosome 22, also called del22) and cancers such as chronic myelogenous leukemia (a translocation involving chromosomes 9 and 22).

III. Comparative genomic hybridization

Comparative genomic hybridisation (CGH) is a technique that permits the detection of chromosomal copy number changes without the need for cell culturing. It provides a global overview of chromosomal gains and losses throughout the whole genome of a tumour. Tumour DNA is labelled with a green fluorochrome, which is subsequently mixed (1:1) with red labelled normal DNA and hybridised to normal human metaphase preparations. The green and red labelled DNA fragments compete for hybridisation to their locus of origin on the chromosomes. The green to red fluorescence ratio measured along the chromosomal axis represents loss or gain of genetic material in the tumour at that specific locus. In addition to a fluorescence microscope, the technique requires a computer with dedicated image analysis software to perform the analysis.