Short tandem repeat (STR) analysis

DEFINITION: Determination of the number of repetitive DNA sequences two to six 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 other DNA identification method based on variable number of tandem repeats (VNTRs) and restriction fragment length polymorphism (RFLP) analysis, popularized by DNA fingerprinting that emerged in the mid-1980s. 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 on  DNA that were typically ten to hundred base pairs in length, also called minisatellites. This process is also referred to as the analysis 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. Next-generation sequencing (NGS) uses an extensive parallel sequencing to enable accurate identification, simplify managing short-read and long-read sequencing data, and reduce costs.

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.

STR finds extensive applications in cases of unidentified remains, determining parentage, crime scene investigations, and missing person cases by mapping specific core sets of loci against those in the Combined DNA Index System (CODIS) used by US law enforcement organizations.

Bibliography

“Biometrics and Fingerprints.” FBI.gov, le.fbi.gov/science-and-lab/biometrics-and-fingerprints/codis-2. Accessed 9 Jan. 2026.

Chaushevska, M., et al. “Get Ready for Short Tandem Repeats Analysis Using Long Reads–The Challenges and the State of the Art.” Frontiers in Genetics, 2025, doi.org/10.3389/fgene.2025.1610026. Accessed 9 Jan. 2026.

Griffiths, Anthony J. F., et al. Introduction to Genetic Analysis. 9th ed., W. H. Freeman, 2007.

National Institute of Justice. “DNA Typing by RFLP Analysis.” Crime Scene and DNA Basics for Forensic Analysts, 16 June 2023, nij.ojp.gov/nij-hosted-online-training-courses/crime-scene-and-dna-basics-forensic-analysts/history-and-types-forensic-dna-testing/dna-typing-rflp-analysis. Accessed 9 Jan. 2026.

National Institute of Standards and Technology. “Short Tandem Repeats Str.” OSAC Lexicon, 12 June 2023, www.nist.gov/glossary-term/31936. Accessed 9 Jan. 2026.

Strachan, Tom, and Andrew P. Read. Human Molecular Genetics 3. Garland, 2004.

Van Campen, Julia. “Short Tandem Repeat (STR) Testing.” National Health Service England, 10 Feb. 2025, www.genomicseducation.hee.nhs.uk/genotes/knowledge-hub/short-tandem-repeat-str-testing/. Accessed 9 Jan. 2026.