Brief Introduction to STRs
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Background Information Regarding Short Tandem Repeats and DNA Typing
[Advantages over RFLP] [Commonly Used STR Loci] [Nomenclature Issues]
Tandemly repeated DNA sequences are widespread throughout the human genome and show sufficient variability among individuals in a population that they have become important in several fields including genetic mapping, linkage analysis, and human identity testing. These tandemly repeated regions of DNA are typically classified into several groups depending on the size of the repeat region. Minisatellites (variable number of tandem repeats, VNTRs) have core repeats with 9-80 bp, while microsatellites (short tandem repeats, STRs) contain 2-5 bp repeats. The forensic DNA community has moved primarily towards tetranucleotide repeats, which may be amplified using the polymerase chain reaction (PCR) with greater fidelity than dinucleotide repeats. The variety of alleles present in a population is such that a high degree of discrimination among individuals in the population may be obtained when multiple STR loci are examined.
Advantages of STRs over traditional RFLP techniques
PCR-based STRs have several advantages over conventional Southern blotting techniques of the larger variable number tandem repeats (VNTRs). Discrete alleles from STR systems may be obtained due to their smaller size, which puts them in the size range where DNA fragments differing by a single basepair in size may be differentiated. Determination of discrete alleles allows results to be compared easily between laboratories without binning. In addition, smaller quantities of DNA, including degraded DNA, may be typed using STRs. Thus, the quantity and integrity of the DNA sample is less of an issue with PCR-based typing methods than with conventional RFLP methods. For a review article on genetic identity testing using STRs, see link to http://www.promega.com/pnotes/58/5189c/5189c.html.
STR Loci Commonly Used in DNA Typing
There are literally hundreds of STR systems which have been mapped throughout the human genome {132}. Several dozen have been investigated for application to human identity testing {3-5}. These STR loci are found on almost every chromosome in the genome. They may be amplified using a variety of PCR primers. Tetranucleotide repeats have been most popular among forensic scientists due to their fidelity in PCR amplification although some tri- and pentanucleotide repeats are also in use {1,5}.
Desirable features for STR systems include
- high heterozygosity
- regular repeat unit
- distinguishable alleles
- robust amplification
There are several types of STRs which have been classified by Urquhart et al. {5,92}:
- Simple consisting of 1 repeating sequence: FES/FPS
- Simple with nonconsensus alleles: HUMTH01, F13A1
- Compound consisting of 2 or more different repeat sequences: GABRB15
- Compound with nonconsensus alleles: VWA
- Complex repeats: D21S11
- Hypervariable repeats: SE33
Comment on Nomenclature for STR Alleles and Repeat Structure
In October 1993, the DNA Commission of the International Society of Forensic Haemogenetics (ISFH) recommended the nomenclature for STR systems which is commonly used today {9}. Alleles are generally named by the number of repeats which they contain. When an allele does not conform to the standard repeat motif of the system in question, it should be designated by the number of complete repeat units and the number of base pairs of the partial repeat. These two values should be separated by a decimal point {9}. For example, the STR locus HUMTH01 contains a nonconsensus allele which is relatively common in Caucasians. This allele is 1 bp shorter than 10 repeat units, due to the loss of an adenine in the 7th repeat unit {30,76}, and is thus designated 9.3. The ISFH also recommends using allelic ladders containing the commonly occurring alleles and establishing the size and sequence of those alleles through sequencing.
It is important to point out that the nomenclature used by Dr. Caskey and coworkers {3,121}, and now Promega Corporation (see their STR workbook, {364}), does not always follow the sequence data in GenBank. Reading the literature and trying to compare results between laboratories around the world may be confusing without understanding this issue. For example, descriptions of the STR system HUMTH01 by one group often list the core repeat structure as having an AATG repeat {3} while other groups have followed the GenBank sequence format, use the other DNA strand, and label the repeat TCAT {4,69}. Some kind of consensus should be reached by the DNA typing community to make comparison of results easier. We recommend that the core repeat structure be designated from the DNA strand contained in GenBank, as it is publicly available.
*Note*: The numbers in brackets { } indicate a reference in the complete STR reference listing contained in this database.
Purpose of This STR Database and Web Page
While the use of STRs for genetic mapping and identity testing has become widespread among DNA typing laboratories, there is no single place where information may be found regarding STR systems. This web site is an attempt to bring together the abundant literature on the subject in a cohesive fashion to make future work in this field easier. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included in this database. Addresses for scientists working in this area have also been included as well as a comprehensive reference listing of material on STRs used for DNA typing purposes.
If you or someone you know has additional information which would supplement the data included here, please contact us.
Last Updated: 07/05/2007