Short tandem repeat (STR) analysis
Short tandem repeat (STR) analysis is a method used to determine the number of specific repeating DNA sequences, typically consisting of two to seven base pairs, at designated locations on chromosomes. This technique has become a crucial tool for identifying individuals based on DNA samples, with applications in criminal investigations, paternity testing, and identifying human remains. Since its rise to prominence in the 1990s, STR analysis has largely replaced the older restriction fragment length polymorphism (RFLP) method due to its efficiency and effectiveness. STR analysis requires significantly smaller amounts of DNA—about one hundred times less than RFLP—and can be completed within a few hours. The integration of polymerase chain reaction (PCR) amplifies trace DNA samples, making the process more robust against degradation.
While STR analysis offers many advantages, such as reduced sensitivity to DNA degradation, it has a limitation in that the variability of shorter DNA fragments is less than that of longer fragments used in RFLP analysis. To address this limitation, multiplex systems have been developed, enabling the simultaneous analysis of multiple DNA fragments labeled with fluorescent dyes. Further enhancements, like capillary gel electrophoresis, have improved the speed and efficiency of the analysis, making STR a vital component in modern forensic science and genetic testing.
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Short tandem repeat (STR) analysis
DEFINITION: Determination of the number of repetitive DNA sequences two to seven base pairs in length that are found at particular locations on chromosomes in long arrays, the exact number of which typically varies among individuals in a population.
SIGNIFICANCE: Short tandem repeat analysis represents a rapid and straightforward way to identify the persons to whom samples of DNA belong and is widely used for the identification of DNA samples collected at crime scenes, in paternity testing, and in the identification of human remains.
Since the 1990s, the analysis of short tandem repeats (STRs; also called microsatellites) as a method of DNA (deoxyribonucleic acid) identification has gained prominence over the original Restriction fragment length polymorphism (RFLP) protocol developed in 1985. The original method required that a relatively large amount of nondegraded DNA (about 100 nanograms) be isolated from a forensic sample and took several days to process. It measured the variation in the number of repeating units of DNA that were typically fifteen to fifty base pairs in length, also called minisatellites. This process is also referred to as the analysis of variable number of tandem repeats (VNTRs).
STR analysis has several advantages over the RFLP protocol: It requires about one hundred times less DNA, it can be completed within a few hours, and it exhibits less sensitivity to DNA degradation. The first two advantages come about mainly because of the coupling of this procedure with the polymerase chain reaction (PCR), also developed during the 1980s. PCR allows for the rapid amplification of trace amounts of DNA using a set of DNA “primers” that bind to the sequence of interest and use it as a template to make millions of copies. The final advantage is the result of the decreased size of the DNA fragments that are analyzed, typically only a few hundred base pairs in length. It follows that, as the length of DNA being analyzed decreases, so does the probability that it has been degraded.
The short length of the fragments used in STR analysis does introduce one limitation. Because the variability in these shorter fragments within a population is less compared with RFLP analysis, more of them must be analyzed to provide the same assurances of an exact identification. This drawback has been circumvented by the development of “multiplex” systems for PCR. Here eight to sixteen pairs of PCR primers are combined in one reaction, each set labeled with a different fluorescent dye so that the products can be discriminated.
Another modification that has been made to improve STR analysis is the use of capillary gel electrophoresis, instead of the traditional “slab” gels, to separate out the resulting DNA fragments. This technique, developed in conjunction with the Human Genome Project, which was completed in 2003, is much faster than slab gels and particularly amenable to the use of fluorescently labeled primers.
Bibliography
Griffiths, Anthony J. F., et al. Introduction to Genetic Analysis. 9th ed. New York: Freeman, 2008. Print.
Strachan, Tom, and Andrew P. Read. Human Molecular Genetics 3. New York: Garland, 2004. Print.
Van Campen, Julia. "Short Tandem Repeat (STR) Testing." National Health Service England, 15 Nov. 2022, www.genomicseducation.hee.nhs.uk/genotes/knowledge-hub/short-tandem-repeat-str-testing/. Accessed 18 Aug. 2024.