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Short tandem repeat typing technologies used in human identity testing
 
John M. Butler
Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
BioTechniques, Vol. 43, No. 4, October 2007, pp. Sii–Sv
Full Text (PDF)
Abstract

Short tandem repeat (STR) typing methods are widely used today for human identity testing applications including forensic DNA analysis. Following multiplex PCR amplification, DNA samples containing the length-variant STR alleles are typically separated by capillary electrophoresis and genotyped by comparison to an allelic ladder supplied with a commercial kit. This article offers a brief perspective on the technologies and issues involved in STR typing.

Introduction

Short tandem repeats (STRs), which are sometimes referred to as microsatellites or simple sequence repeats (SSRs), are accordion-like stretches of DNA containing core repeat units of between two and seven nucleotides in length that are tandemly repeated from approximately a half dozen to several dozen times (1). Although the human genome contains thousands upon thousands of STR markers, only a small core set of loci have been selected for use in forensic DNA and human identity testing (2). Like using a single, common currency in a financial sense, core loci permit equivalent genetic information to be shared and compared. Commercial kits are now available to generate DNA profiles containing these core STR loci (Table 1). Millions of STR profiles are generated worldwide each year by government, university, and private laboratories performing various forms of human identity testing, including DNA databasing, forensic casework, missing persons/mass disaster victim identification, or parentage testing.



With STR typing, PCR is used to recover information from small amounts of available biological material. The relatively short PCR product sizes of approximately 100–500 bp generated with STR testing are generally compatible with degraded DNA that may be present due to environmental insults on the evidentiary biological material found at a crime scene. PCR amplification of multiple STR loci simultaneously, or multiplexing, is possible with different colored fluorescent dyes and different sized PCR products. Use of multiple loci enables a high power of discrimination in a single test without consuming much DNA (e.g., 1 ng or less of starting material). It is worth noting that these core STR loci occur in between genes in which a high degree of variability is tolerated and are thus not directly responsible for physical traits such as hair color or eye color or genetic diseases.

Commercial Kits

Commercially available kits, which provide premixed primers and a standard master mixture containing the polymerase, enzyme buffers, and dNTPs, simplify generation of STR profiles and provide results on a uniform set of core STR loci to make it possible for national and international sharing of criminal DNA profiles. Commercial kits are preferred in most forensic laboratories over in-house assays even though the kits are more expensive, as these kits help simplify and standardize procedures and remove the burden of PCR component quality control from the busy end user. In addition, STR kits supply allelic ladders containing common STR alleles that have been previously characterized for the number of repeat units via DNA sequencing. These allelic ladders are used to calibrate PCR product sizes to STR repeat number for genotyping purposes. Figure 1 shows the allelic ladder for the widely used AmpFlSTR Identifiler kit (Applied Biosystems, Foster City, CA, USA) (3) containing 205 alleles across 16 coamplified loci—15 STRs plus an amelogenin sex-typing assay.



The complete process for STR typing includes sample collection, DNA extraction, DNA quantitation, PCR amplification of multiple STR loci, STR allele separation and sizing, STR typing and profile interpretation, and a report of the statistical significance of a match (if observed). In many casework situations, such as sexual assault evidence, DNA mixtures may result from a combination of the victim and perpetrator's bodily fluids and create a complex and challenging result to interpret.

DNA Separations

Following PCR amplification, the overall length of the STR amplicon is measured to determine the number of repeats present in each allele found in the DNA profile. This length measurement is made via a sized-based separation involving gel or capillary electrophoresis (CE). Each STR amplicon has been fluorescently labeled during PCR, since either the forward or reverse locus-specific primer contains a fluorescent dye. Thus, by recording the dye color and migration time of each DNA fragment relative to an internal size standard, the size for each STR allele may be determined following its separation from other STR alleles. Commonly used instruments for STR allele separation and sizing include the ABI PRISM 310 and ABI PRISM 3100 genetic analyzers (Applied Biosystems) (4).

There are a number of both biological and instrumental artifacts that often must be sorted through in order to generate a complete and accurate STR profile (5,; see also Reference 1, Chapters 6 and 15). Biological artifacts include stutter products, split peaks from incomplete adenylation, triallelic patterns, and variant alleles containing mutations in the repeat or flanking regions that cause an allele to be off-ladder. Instrumental artifacts arise from voltage spikes, dye blobs, and bleed-through between dye colors.

While multicolor fluorescence detection CE instrumentation, such as the ABI PRISM 3100 genetic analyzer, presently dominate the field, efforts are ongoing to develop microchip CE platforms (6) to perform high-resolution DNA separations with eventual integration of the PCR amplification and CE separations (7). In addition, mass spectrometry (MS) with matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) techniques have been used for STR typing without allelic ladders (8,9).

miniSTRs: Recovery of Information From Degraded DNA

DNA molecules that are exposed to water and/or heat will, over time, begin to break down into smaller pieces. A number of studies have shown what is theoretically predicted—that DNA types can be recovered more effectively from degraded DNA samples when the PCR products are smaller (10,11,12). By moving the PCR primers closer to the STR repeat region, the product sizes can be reduced while retaining the same information (11). The utility of miniSTR assays has been confirmed in intra- and interlaboratory studies involving degraded bone samples and aged blood and saliva stains (12). Success rates in recovering information from compromised DNA samples improve with miniSTR systems compared with conventional STR kits. A timeline covering the development of miniSTRs may be found at www.cstl.nist.gov/biotech/strbase/miniSTR/timeline.htm.

Using their 5-dye chemistry and mobility modifier technology, Applied Biosystems has developed a miniSTR kit capable of amplifying eight core STR loci and amelogenin with reduced PCR product sizes relative to current commercial kits. This AmpFlSTR MiniFiler kit, which includes an improved PCR master mixture, should aid efforts to recover results from degraded DNA samples. However, it is important to keep in mind that because different PCR primers are in use with the miniSTR kit relative to previous STR kits, discordant results may occur due to primer binding site mutations that cause allele dropout.

Concordance Testing

Some STR alleles contain sequence variation in the flanking regions. If a nucleotide change (or insertion or deletion) occurs in a PCR primer binding site in a particular allele, then it is possible for the mutant sequence to be incompatible with primer annealing and the variant allele will fail to amplify (1). This allelic dropout is sometimes referred to as a null allele. A sample that is really a heterozygote might show up as an apparent homozygote if the PCR primers fail to anneal and amplify the allele containing the point mutation (Figure 2). In some cases, the null allele may be recovered by lowering the annealing temperature, permitting less stringent binding between the primer and DNA template. A concordance study, which tests a set of the same DNA samples with nonoverlapping PCR primers, permits detection of null alleles. An examination of MiniFiler versus Identifiler found only 27 discrepancies in over 10,000 genotypes compared (13). A summary of discordant results observed in concordance studies is available at www.cstl.nist.gov/biotech/strbase/NullAlleles.htm.



As long as the same PCR primers are used, identical STR typing results can be expected on the same DNA sample. However, if primer positions are changed, then the possibility exists for allele dropout or size shifting to occur. In some cases, extra primers matching the mutant allele—often referred to as degenerate primers—can be including in the kit primer mixture to enable recovery of PCR amplification when the variant allele containing a mismatch in the primer binding site is present (14).

Perspectives on The Future

As noted almost 7 years ago by the Research and Development Working Group of the National Commission on the Future of DNA Evidence (15), STRs will probably be the markers of choice for the foreseeable future because of their widespread use in national DNA databases (2,16,17). We will likely see evolutionary progression in typing technology, more rapid amplification methods, additional STR kits containing new loci, and computer programs that will enable fast evaluation of STR typing data. Through continued advances, STR typing technologies may become miniaturized and integrated with other parts of the process, such as DNA extraction and amplification. Effective DNA databases are being constructed and numerous forensic cases solved today through generating STR profiles with a common set of genetic markers. These current core loci have played and will continue to play a vital role in human identity testing.

Acknowledgments

The author, John M. Butler, is funded by the National Institute of Justice through interagency agreement 2003-IJ-R-029 with the National Institute of Standards and Technology (NIST) Office of Law Enforcement Standards. Points of view in this document are those of the author and do not necessarily represent the official position or policies of the U.S. Department of Justice. Certain commercial equipment, instruments, and materials are identified to specify experimental procedures as completely as possible. In no case does such identification imply a recommendation or endorsement by the NIST nor does it imply that any of the materials, instruments, or equipment identified are necessarily the best available for the purpose. Comments on this manuscript by Peter Vallone (NIST Human Identity Project Team) were greatly appreciated.

Competing Interests Statement

The author declares no competing interests.

References
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