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The field of clinical cytogenetics and the description of syndromes caused by gross chromosomal abnormalities laid the foundation for defining and delineating malformation syndromes. Chromosomal abnormalities are detected in approximately 1 in 110 newborns and are the common most single cause of mental retardation or developmental delay.1,2 The common pediatric indications for a chromosome analysis include growth retardation, neurologic impairment, neuropsychological dysfunction, ambiguous genitalia, or multiple congenital anomalies. Clinical cytogenetics also, in part, laid the foundation of the field of dysmorphology. This chapter provides the principles of human cytogenetics.

Cytogenetics is a whole genome analysis involving the examination of chromosomes from a tissue of interest to identify large-scale genomic alterations. This occurs through the microscopic examination of chromosomes arrested during the metaphase stage of cell division. The chromosomes are treated with enzymes and chemicals to produce characteristic light and dark patterns, called bands, along the arms of the chromosomes. Each of the 46 chromosomes can then be identified individually and organized into a karyogram (the ordered display of chromosomes, eFig. 173.1) and described as a karyotype (the nomenclature used to describe the results of the chromosome analysis, described in more detail below).

eFigure 173.1.

Normal Giemsa-banded human male karyogram showing each homologous chromosome pair aligned with each other.

The benefits of a chromosome analysis include visualization of the entire genome on a cell-by-cell basis, which allows for the nonselective identification of large-scale alterations in genome structure, as well as detection of mosaicism (the presence of two or more distinct cell populations within an individual). The limitations of this technology include a limit to the size of a genomic abnormality that can be detected. This limit of resolution is about 10 megabases (Mb) but varies according to the region of the genome in which the abnormality occurs and the quality of the chromosome preparations, because abnormalities will be detected only if they alter the banding pattern. Another limitation of a standard chromosome analysis is the need for an actively growing source of cells. At the time of sample acquisition, the majority of cells will not be in metaphase, and therefore, must be cultured, often with chemicals that increase the number of cells in metaphase at the time the cells are harvested and prepared for analysis. As a result, cells that have been fixed or are no longer viable cannot be analyzed with this technology.


Normally, each human has 46 chromosomes that are distributed in 23 pairs, 22 pairs of autosomes and 1 pair of sex chromosomes (XX in females and XY in males). Thus, each individual has two copies of each chromosome (ie, diploid). A normal chromosome constitution is termed the euploid state, whereas an abnormal chromosome complement is called aneuploidy. The autosomes are numbered 1 to 22, with the numbers assigned in descending order ...

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