Cytogenetics is also called chromosome analysis.

Everyone has 23 pairs of chromosomes, 22 pairs of autosomes and one pair of sex chromosomes. The science that relates to the study of these chromosomes is referred to as “cytogenetics". Persons who look at chromosome preparations on slides are “cytogenetic technologists” or "cytogeneticists". A trained cytogeneticist examines the number, shape and staining pattern of these structures using special technologies. In this way, extra chromosomes, missing chromosomes, or rearranged chromosomes can be detected.

Studies of chromosomes begin with the extraction of whole chromosomes from the nuclei of cells. These chromosomes are then placed on glass slides, stained with special stains and examined under a microscope. Sometimes, pictures are taken of the chromosomes on the slides and the picture is cut into pieces so the chromosome pairs can be matched. In recent years, computer software has aided this process. Each chromosome pair is assigned special number (from 1 to 22, then X and Y) that is based on their staining pattern and size.

There are many disorders that can be diagnosed by examining a person’s whole chromosomes. Down syndrome, in which an individual has an extra chromosome 21, can be determined by cytogenetic studies. When there are three chromosomes in one group instead of a pair, it is referred to as a “trisomy". Missing chromosomes can also be detected, as in the case of Turner’s syndrome, in which a female has only a single X chromosome. When there is only one chromosome instead of a pair, it is referred to as a “monosomy".

Abnormalities in chromosome structure are also observed with cytogenetic staining techniques. The Fragile X syndrome, the most common inherited cause of mental retardation, takes its name from the appearance of the stained X chromosome under a microscope. There is a site near the end of this chromosome that does not stain, indicating its fragility. The gene in the fragile region is important in making a special protein needed by developing brain cells.

Sometimes, pieces of a chromosome will break off and attach to another chromosome somewhere in a person’s genome. When this happens, it is referred to as a “translocation". An example of a disease caused by a translocation would be chronic myeloid leukaemia (CML) in which a part of chromosome 9 breaks off and attaches itself to chromosome 22. Another example would be Burkitt’s lymphoma, in which a piece of chromosome 8 attaches to chromosome 14. These chromosomal translocations cause disease because the broken piece usually attaches to the new chromosome near a special gene that then becomes activated and turns normal cells into tumour cells. Translocations can sometimes be seen under the microscope if a special stain is used. Some individuals carry translocations that do not affect the genes within these chromosomes i.e. no chromosomal material is lost or gained. These translocations do not usually have any adverse effects.

A special technique called fluorescent in situ hybridisation or FISH can be used to view changes in chromosomes that result from genetic variations. A mutated gene segment in a chromosome can be made to “light up” or fluoresce when it is bound by a special probe. Genetic changes in some cancers can be detected using this method. For instance, FISH is one of the methods used to determine increased expression of the gene HER2/neu. There are many other applications of FISH technology as well, such as chromosome microdeletions, in which a certain part of a chromosome is completely missing. In this case, the chromosome segment will not fluoresce compared to a normal set of chromosomes. FISH is also used as the first test to look for extra or missing chomosomes when a pregnant woman has an amniocentesis or chorionic villus sampling to look for e.g. Down syndrome.

Microarray testing is an advance in technology that allows detection of chromosome imbalances that are smaller than can be detected by looking down a microscope. These smaller imbalances are called microdeletions or microinsertions. Despite their smaller size, they can still cause major birth defects and genetic syndromes. Microarray testing does not require the cells to be grown before the test can be performed so, like FISH testing, it can be done much faster than conventional chromosome analysis.