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Butler (STR Review)
Butler (STR Review)
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 testing are generally compatible with the burden of PCR component quality
degraded DNA that may be present control from the busy end user. In
Short tandem repeats (STRs), which due to environmental insults on the addition, STR kits supply allelic ladders
are sometimes referred to as micro- evidentiary biological material found containing common STR alleles that
satellites or simple sequence repeats at a crime scene. PCR amplification have been previously characterized for
(SSRs), are accordion-like stretches of multiple STR loci simultaneously, the number of repeat units via DNA
of DNA containing core repeat units or multiplexing, is possible with sequencing. These allelic ladders are
of between two and seven nucleotides different colored fluorescent dyes and used to calibrate PCR product sizes
in length that are tandemly repeated different sized PCR products. Use of to STR repeat number for genotyping
from approximately a half dozen to multiple loci enables a high power of purposes. Figure 1 shows the allelic
several dozen times (1). Although the discrimination in a single test without ladder for the widely used AmpFlSTR
human genome contains thousands consuming much DNA (e.g., 1 ng or Identifiler kit (Applied Biosystems,
upon thousands of STR markers, only a less of starting material). It is worth Foster City, CA, USA) (3) containing
small core set of loci have been selected noting that these core STR loci occur in 205 alleles across 16 coamplified
for use in forensic DNA and human between genes in which a high degree loci—15 STRs plus an amelogenin
identity testing (2). Like using a single, of variability is tolerated and are thus sex-typing assay.
common currency in a financial sense, not directly responsible for physical The complete process for STR
core loci permit equivalent genetic traits such as hair color or eye color or typing includes sample collection,
information to be shared and compared. genetic diseases. DNA extraction, DNA quantitation,
Commercial kits are now available to PCR amplification of multiple STR
generate DNA profiles containing these COMMERCIAL KITS loci, STR allele separation and sizing,
core STR loci (Table 1). Millions of STR typing and profile interpretation,
STR profiles are generated worldwide Commercially available kits, and a report of the statistical signifi-
each year by government, university, which provide premixed primers and cance of a match (if observed). In many
and private laboratories performing a standard master mixture containing casework situations, such as sexual
various forms of human identity the polymerase, enzyme buffers, assault evidence, DNA mixtures may
testing, including DNA databasing, and dNTPs, simplify generation of result from a combination of the victim
forensic casework, missing persons/ STR profiles and provide results on a and perpetrator’s bodily fluids and
mass disaster victim identification, or uniform set of core STR loci to make it create a complex and challenging result
parentage testing. possible for national and international to interpret.
With STR typing, PCR is used sharing of criminal DNA profiles.
to recover information from small Commercial kits are preferred in most DNA SEPARATIONS
amounts of available biological forensic laboratories over in-house
material. The relatively short PCR assays even though the kits are more Following PCR amplification, the
product sizes of approximately expensive, as these kits help simplify overall length of the STR amplicon is
100–500 bp generated with STR and standardize procedures and remove measured to determine the number of
Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
Table 1. Characteristics of the 15 STR Loci Present in the Commercially Available Kit AmpFlSTR Identifiler
PCR Product Sizes in
STR Loci Chromosomal Location Repeat Motif Allele Rangea Identifiler Kit
(dye label)
CSF1PO 5q33.1 TAGA 6–15 305–342 bp (6-FAM)
FGA 4q31.3 CTTT 17–51.2 215–355 bp (PET)
TH01 11p15.5 TCAT 4–13.3 163–202 bp (VIC)
TPOX 2p25.3 GAAT 6–13 222–250 bp (NED)
VWA 12p13.31 [TCTG] [TCTA] 11–24 155–207 bp (NED)
D3S1358 3p21.31 [TCTG] [TCTA] 12–19 112–140 bp (VIC)
D5S818 5q23.2 AGAT 7–16 134–172 bp (PET)
D7S820 7q21.11 GATA 6–15 255–291 bp (6-FAM)
D8S1179 8q24.13 [TCTA] [TCTG] 8–19 123–170 bp (6-FAM)
D13S317 13q31.1 TATC 8–15 217–245 bp (VIC)
D16S539 16q24.1 GATA 5–15 252–292 bp (VIC)
D18S51 18q21.33 AGAA 7–27 262–345 bp (NED)
D21S11 21q21.1 [TCTA] [TCTG] 24–38 185–239 bp (6-FAM)
D2S1338 2q35 [TGCC] [TTCC] 15–28 307–359 bp (VIC)
D19S433 19q12 AAGG 9–17.2 102–135 bp (NED)
Xp22.22 X = 107 bp (PET)
Amelogenin (sex-typing) Not applicable Not applicable
Yp11.2 Y = 113 bp (PET)
The 13 core STR loci used for the U.S. national DNA database are shown in bold font. See www.cstl.nist.gov/biotech/strbase/multiplx.htm for information on
other commercially available STR kits.
aRanges are calculated from kit allelic ladders (see Figure 1) and do not represent the full range of alleles observed in world populations. A more complete allele
and integrated with other parts of 4. Butler, J.M., E. Buel, F. Crivellente, and UK—past, present, and future perspectives.
the process, such as DNA extraction B.R. McCord. 2004. Forensic DNA typing BioTechniques 32:366-372.
by capillary electrophoresis: using the ABI 17. Gill, P., D.J. Werrett, B. Budowle, and R.
and amplification. Effective DNA Prism 310 and 3100 Genetic Analyzers for Guerrieri. 2004. An assessment of whether
databases are being constructed and STR analysis. Electrophoresis 25:1397-1412. SNPs will replace STRs in national DNA
numerous forensic cases solved today 5. Scientific Working Group on DNA Analysis databases—joint considerations of the DNA
through generating STR profiles with a Methods (SWGDAM). 2000. Short tan- working group of the European Network of
dem repeat (STR) interpretation guidelines. Forensic Science Institutes (ENFSI) and the
common set of genetic markers. These Forensic Sci. Comm. 2(3); online at www.fbi. Scientific Working Group on DNA Analysis
current core loci have played and will gov/hq/lab/fsc/backissu/july2000/strig.htm. Methods (SWGDAM). Sci. Justice 44:51-53.
continue to play a vital role in human 6. Yeung, S.H., S.A. Greenspoon, A.
identity testing. McGuckian, C.A. Crouse, C.A. Emrich,
J. Ban, and R.A. Mathies. 2006. Rapid and
Address correspondence to John M. Butler,
high-throughput forensic short tandem repeat
typing using a 96-lane microfabricated cap- Biochemical Science Division, National
ACKNOWLEDGMENTS illary array electrophoresis microdevice. J. Institute of Standards and Technology,
Forensic Sci. 51:740-747. 100 Bureau Drive, Mail Stop 8311,
The author, John M. Butler, is fund- 7. Liu, P., T.S. Seo, N. Beyor, K.J. Shin, J.R. Gaithersburg, MD 20899-8311, USA.
ed by the National Institute of Justice Scherer, and R.A. Mathies. 2007. Integrated
portable polymerase chain reaction-capillary e-mail: john.butler@nist.gov
through interagency agreement 2003- electrophoresis microsystem for rapid foren-
IJ-R-029 with the National Institute sic short tandem repeat typing. Anal. Chem.
of Standards and Technology (NIST) 79:1881-1889. To purchase reprints of this article, contact:
Office of Law Enforcement Standards. 8. Butler, J.M., J. Li, T.A. Shaler, J.A. Reprints@BioTechniques.com
Points of view in this document are Monforte, and C.H. Becker. 1998. Reliable
genotyping of short tandem repeat loci with-
those of the author and do not neces- out an allelic ladder using time-of-flight mass
sarily represent the official position spectrometry. Int. J. Legal Med. 112:45-49.
or policies of the U.S. Department of 9. Oberacher, H., F. Pitterl, G. Huber, H.
Justice. Certain commercial equip- Niederstatter, M. Steinlechner, and W.
Parson. Increased forensic efficiency of DNA
ment, instruments, and materials are fingerprints through simultaneous resolution
identified to specify experimental pro- of length and nucleotide variability by high-
cedures as completely as possible. In performance mass spectrometry. Hum. Mutat.
no case does such identification imply (In press).
a recommendation or endorsement by 10. Wiegand, P. and M. Kleiber. 2001. Less is
more—length reduction of STR amplicons
the NIST nor does it imply that any of using redesigned primers. Int. J. Legal Med.
the materials, instruments, or equip- 114:285-287.
ment identified are necessarily the best 11. Butler, J.M., Y. Shen, and B.R. McCord.
available for the purpose. Comments 2003. The development of reduced size STR
amplicons as tools for analysis of degraded
on this manuscript by Peter Vallone DNA. J. Forensic Sci. 48:1054-1064.
(NIST Human Identity Project Team) 12. Dixon, L.A., A.E. Dobbins, H.K. Pulker,
were greatly appreciated. J.M. Butler, P.M. Vallone, M.D. Coble, W.
Parson, B. Berger, et al. 2006. Analysis of
artificially degraded DNA using STRs and
COMPETING INTERESTS SNPs—results of a collaborative European
(EDNAP) exercise. Forensic Sci. Int.
STATEMENT 164:33-44.
13. Hill, C.R., M.C. Kline, J.J. Mulero, R.E.
The author declares no competing Lagace, C.W. Chang, L.K. Hennessy, and
interests. J.M. Butler. 2007. Concordance study be-
tween the AmpFlSTR MiniFiler PCR ampli-
fication kit and conventional STR typing kits.
J. Forensic Sci. 52:870-873.
REFERENCES 14. Leibelt, C., B. Budowle, P. Collins, Y.
Daoudi, T. Moretti, G. Nunn, D. Reeder,
1. Butler, J.M. 2005. Forensic DNA Typing: and R. Roby. 2003. Identification of a
Biology, Technology, and Genetics of STR D8S1179 primer binding site mutation and
Markers. 2nd ed. Elsevier Academic Press, the validation of a primer designed to recover
New York. null alleles. Forensic Sci. Int. 133:220-227.
2. Butler, J.M. 2006. Genetics and genomics of 15. National Institute of Justice (NIJ). 2000.
core STR loci used in human identity testing. The future of forensic DNA testing: pre-
J. Forensic Sci. 51:253-265. dictions of the Research and Development
3. Collins, P.J., L.K. Hennessy, C.S. Leibelt, Working Group of the National Commission
R.K. Roby, D.J. Reeder, and P.A. Foxall. on the Future of DNA Evidence. Washington,
2004. Developmental validation of a single- D.C. www.ojp.usdoj.gov/nij/pubs-sum/
tube amplification of the 13 CODIS STR loci, 183697.htm.
D2S1338, D19S433, and amelogenin: the 16. Gill, P. 2002. Role of short tandem
AmpFlSTR Identifiler PCR Amplification repeat DNA in forensic casework in the
Kit. J. Forensic Sci. 49:1265-1277.