STRs — Ideal for Human Identification

Agnes Caruso, Product Manager at Canon BioMedical on August 6, 2018

 

What are STRs?

Microsatellites, also known as Short Tandem Repeats (STRs), are stretches of DNA that are made up of two to six nucleotides-long repeats adjacent to each other (1). The stretches of repeats are variable in length, from a few to hundreds of repeats. The most useful for STR typing are loci ranging between 10 and 30 repeats. STRs are present in non-coding DNA sequences and distributed approximately every 10,000 base pairs along the chromosomes. These sequences are highly polymorphic with multiple alleles of each present in a given population.  Everyone inherits one allele of an STR from each parent. The two inherited alleles may be similar or not in the number of repeats.

STRs are classified based on size, type, and location in the genome. The pattern of repeats can be:

  • Simple, where all repeat units are identical
  • Compound, with two or more adjacent simple repeats
  • Complex, if the repeats are of different sequence and length.

Chromosomal location of microsatellites is very important not just for classification, but also for using them in different applications. The largest group contains autosomal STRs, composed of regular and mini-STRs, which are inherited from both parents. Y-STRs are inherited solely in the paternal line, from father to sons, thus they are not unique between family members. Mitochondrial DNA (mtDNA), on the other hand, is inherited only from a mother by children of both sexes. An advantage of mtDNA is also its high copy number making it useful in cases where starting sample amount is limited.

STR Typing

A power of STR typing lies in the concurrent analysis of multiple loci. The most useful markers for this analysis are those with the highest variability. It is a common practice to amplify 11 to 17 different loci. When a single STR is tested, 5 to 20% of individuals can share a particular allele. However, when, for example, 13 STRs are tested, a probability of a random match is less than one in a trillion (2). Considering that there are some 7.5 billion people on earth, this allows accurate identification of an individual.

Sample types for testing can be varied and include blood, saliva, buccal cells collected with swabs, blood spots, sperm, vaginal swabs, fingernail clippings, hair, blood stains or “touch DNA” samples. Some of these can be badly degraded or offer a very limited amount of DNA. In most cases, DNA has to be extracted from the samples prior to amplification (3,4).

When the starting material is limiting, there are a number of methods that can be used to allow for sample typing. One of the methods is direct amplification from sample materials. Additional methods involve using mini-STRs, which are shorter amplicons compared to regular STRs (5), or using mtDNA, present in a cell in high copy number. An mtDNA profile can be theoretically obtained from a single cell.

After DNA extraction, the sample is quantified and then microsatellites are amplified by multiplex PCR, with fluorescently-labeled primers (6). The generated fragments are subsequently separated using capillary electrophoresis. Alleles are then assigned to peaks based on size. Once a profile is obtained, it is compared to another profile or a search is performed in a database for a match, and match probability is calculated.

 

Applications

STRs are the primary genetic markers used for human identity testing, in forensic applications, missing persons, paternity testing, or natural disasters. They are also used in the study of evolution and lineage (7). Other applications include cell line verification, testing for genetic diseases caused by expansion of repeats, loss of heterozygosity (LOH) in cancer testing, or monitoring chimerism post-transplant. STRs are not only used in human studies but also in plant and animals.

Forensic applications are probably the most commonly known due to TV shows, such as CSI. In the US, the STR profiles are stored in a Combined DNA Index System (CODIS) database. There are 13 “core” STR loci tested by US forensic teams: TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D81179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 (2). Gender is determined by AMEL marker, located on both sex chromosomes. AMEL on X-chromosome is shorter from the copy on Y-chromosome by six base pairs, thus allowing determination of a sample’s gender.

A different but well-established area of use for STR typing is the monitoring of post-transplant chimerism in patients undergoing hemopoietic cell transplant (8). By genotyping recipient and donor white blood cells pre- and post-transplantation a ratio of chimerism is established in a recipient post-transplantation. This ratio determines the level of engraftment of donor cells. One hundred percent donor chimera indicates complete engraftment, while zero percent indicates no donor engraftment.

While STR testing can be developed in-house by a lab, commercially available kits are preferential because:

  • the kits include validated primers
  • the marker multiplexes are optimized
  • a ladder is included in every reaction
  • the kits include a positive DNA control

The use of a commercial kit saves time and effort of optimization. Laboratories are more confident in sharing the data. For forensic applications, the reliability of the method is very important when the data is presented as evidence in court.

STR typing is a simple and efficient method to assess human identity in multiple situations, from paternity, disaster victim identification, forensic work to medical applications in transplantations. Newer methods and equipment have now made STR typing possible from low input samples and shortened the entire workflow. Ultimately, it is the quality of the process and results that are important, to ensure no mistakes are made with the identity of an individual.

Learn more about PCR history and applications by downloading a PCR ebook by The Scientist containing all the basics about PCR sponsored by Canon BioMedical. 

References:

  1. Kupfer, D. M., Huggins, M., Cassidy, B., Vu, N., Burian, D., & Canfield, D. V. (2006). A rapid and inexpensive PCR-based STR genotyping method for identifying forensic specimens(No. DOT-FAA-AM-06-14). FEDERAL AVIATION ADMINISTRATION OKLAHOMA CITY OK CIVIL AEROMEDICAL INST.
  2. Butler, J. M. (2006). Genetics and genomics of core short tandem repeat loci used in human identity testing. Journal of forensic sciences51(2), 253-265.
  3. Solomon, A. D., Hytinen, M. E., McClain, A. M., Miller, M. T., & Dawson Cruz, T. (2018). An optimized DNA analysis workflow for the sampling, extraction, and concentration of DNA obtained from archived latent fingerprints. Journal of forensic sciences63(1), 47-57.
  4. Cavanaugh, S. E., & Bathrick, A. S. (2017). Direct PCR amplification of forensic touch and other challenging DNA samples: A review. Forensic Science International: Genetics.
  5. Hill, C. R., Kline, M. C., Coble, M. D., & Butler, J. M. (2008). Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. Journal of forensic sciences53(1), 73-80.
  6. Butler, J. M. (2004). Short tandem repeat analysis for human identity testing. Current protocols in human genetics41(1), 14-8.
  7. Thompson, R., Zoppis, S., and McCord, B. (2012). An overview of DNA typing methods for human identification: past, present, and future. In DNA Electrophoresis Protocols for Forensic Genetics (pp. 3-16). Humana Press.
  8. Clark, Jordan R., et al. "Monitoring of chimerism following allogeneic haematopoietic stem cell transplantation (HSCT): technical recommendations for the use of Short Tandem Repeat (STR) based techniques, on behalf of the United Kingdom National External Quality Assessment Service for Leucocyte Immunophenotyping Chimerism Working Group." British journal of haematology 168.1 (2015): 26-37.