Microsatellites (also called simple sequence repeats) are a class of genetic polymorphism commonly used for mapping, linkage analysis and to trace inheritance patterns. Microsatellites are tandemly repeated sequences, where the repeating unit is 1 to 4 nucleotides long. The number of times the unit is repeated in a given microsatellite can be highly variable, a characteristic that makes them useful as genetic markers.

Four different kinds of microsatellites are illustrated above. The microsatellite is indicated in upper case letters, and the repeat unit is highlighted in red.
           The majority of microsatellites occur in gene introns or other non-coding regions of the genome; thus variation in the number of repeats has no consequence on gene function. Generally the microsatellite itself does not cause disease, but rather is used as a marker to identify a specific chromosome or locus. When being used as a marker, the specific number of repeats in a given microsatellite is not important, but rather the difference in the number of repeats between alleles. The variation in number of repeats affects the overall length of the microsatellite, a characteristic readily measured by laboratory techniques. Go to Marker Analysis to see how microsatellites are used for this type of analysis.

           The region containing the microsatellite is amplified by PCR using primers (P1 and P2) that flank the microsatellite. The size of the DNA amplified is determined by the number of repeats present in the microsatellite on that allele. The amplified DNA is then run out on a gel that will separate DNA fragments based on size. Individuals typically have two alleles for all microsatellites (the reasons why they would have one are discussed below). If the number of repeats of one allele is different from the other, then two separate bands would show up on the gel.
This figure illustrates microsatellite analysis using four alleles of a microsatellite (A-D). The top figure demonstrate how the total length of the microsatellite varies depending on the number of repeats. The lower figure represents how several possible allele combinations (representing individuals) would look like run out on a gel.
           Sometimes only one allele is visible (such as CC). This could be explained by several possibilities:

  1. Both copies of the microsatellite happen (coincidentally) to have the same number of repeats. When this occurs, a person is said to be homozygous at that marker.
  2. If the microsatellite is located on one of the sex chromosomes (X or Y) and the DNA sample if from a male then only one band would be visible. This is because males only have one copy of the X and Y chromosomes, therefore would only have a single allele for any marker located on those chromosomes.
  3. The individual may have a genetic deletion that includes the region containing the microsatellite. This could be a large deletion, such as complete or partial loss of a chromosome. Or is could be a smaller deletion affecting a single gene or region. When this occurs, the person is said to be hemizygous (has half the genetic material).