Commonly Used Short Tandem Repeat Markers And Commercial Kits

Ever since their discovery in the early 1980s, the ubiquitous occurrence of microsatellites -also referred to as short tandem repeats (STRs) or simple sequence repeats (SSRs)-has puzzled geneticists... [Understanding STRs] is important if we wish to understand how genomes are organized and why most genomes are filled with sequences other than genes.

(Hans Ellegren 2004)


Eukaryotic genomes are full of repeated DNA sequences (see Ellegren 2004). These repeated DNA sequences come in all types of sizes and are typically designated by the length of the core repeat unit and the number of contiguous repeat units or the overall length of the repeat region. Long repeat units may contain several hundred to several thousand bases in the core repeat.

These regions are often referred to as satellite DNA and may be found surrounding the chromosomal centromere. The term satellite arose due to the fact that frequently one or more minor satellite bands were seen in early experiments involving equilibrium density gradient centrifugation (Britten and Kohne 1968, Primrose 1998).

The core repeat unit for a medium length repeat, sometimes referred to as a minisatellite or a VNTR (variant number of tandem repeats), is in the range of approximately 10-100 bases in length (Tautz 1993, Chambers and MacAvoy 2000). The forensic DNA marker D1S80 is a minisatellite with a 16 bp repeat unit and contains alleles spanning the range of 16-41 repeat units (Kasai et al. 1990).

DNA regions with repeat units that are 2-6 bp in length are called microsatellites, simple sequence repeats (SSRs), or short tandem repeats (STRs). STRs have become popular DNA repeat markers because they are easily amplified by the polymerase chain reaction without the problems of differential amplification. This is due to the fact that both alleles from a heterozygous individual are similar in size since the repeat size is small. The number of repeats in STR markers can be highly variable among individuals, which make these STRs effective for human identification purposes.

Figure 5.1

Schematic of minisatellite and microsatellite (STR) DNA markers. PCR primers are designed to target invariant flanking sequence regions. The number of tandem repeat units in the repeat regions varies among individuals making them useful markers for human identification.

Minisatellite Marker (D1S80)

Flanking regions

Flanking regions

STR Marker (TH01)
Str Marker Th01
4 bp repeat unit

Literally thousands of polymorphic microsatellites have been characterized in human DNA and there may be more than a million microsatellite loci present depending on how they are counted (Ellegren 2004). Regardless, microsatellites account for approximately 3% of the total human genome (International Human Genome Sequencing Consortium 2001). STR markers are scattered throughout the genome and occur on average every 10 000 nucleotides (Edwards et al. 1991, Collins et al. 2003, Subramanian et al. 2003). Computer searches of the recently available human genome reference sequence have attempted to comprehensively catalog the number and nature of STR markers in the genome (see Collins et al. 2003, Subramanian et al. 2003). A large number of STR markers have been characterized by academic and commercial laboratories for use in disease gene location studies. For example, the Marshfield Medical Research Foundation in Marshfield, Wisconsin ( has gathered genotype data on over 8000 STRs that are scattered across the 23 pairs of human chromosomes for the purpose of developing human genetic maps (Broman et al. 1998, Ghebranious et al. 2003).

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