The 13 Codis Str Loci

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In the United States, utilization of STRs initially lagged behind that of Europe, especially the efforts of the Forensic Science Service in the United Kingdom. However, beginning in 1996, the FBI Laboratory sponsored a community-wide forensic science effort to establish core STR loci for inclusion within the national DNA database known as CODIS (Combined DNA Index System). Chapter 18 covers CODIS and DNA databases in more detail. This STR Project beginning in April 1996 and concluding in November 1997 involved 22 DNA typing laboratories and the evaluation of 17 candidate STR loci. The evaluated STR loci were CSF1PO, F13A01, F13B, FES/FPS, FGA, LPL, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11.

At the STR Project meeting on 13-14 November 1997, 13 core STR loci were chosen to be the basis of the future CODIS national DNA database (Budowle et al. 1998). The 13 CODIS core loci are CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Table 5.1 lists the original references in the literature for these 13 STRs. When all 13 CODIS core loci are tested, the average random match probability is rarer than one in a trillion among unrelated individuals (Chakraborty et al. 1999). The genetics section of this book provides more information on the calculation of random match probability and evaluation of the 13 CODIS STRs in various populations (see Chapter 20).

The three most polymorphic markers are FGA, D18S51, and D21S11, while TPOX shows the least variation between individuals. A summary of information on the 13 STRs is contained in Table 5.2, which describes the chromosomal

Locus Name

Reference

CSF1PO Hammond, H.A., Jin, L., Zhong, Y., Caskey, C.T. and Chakraborty, R. (1994) Evaluation of 13 short tandem repeat loci for use in personal identification applications. American Journal of Human Genetics, 55, 175-189.

FGA Mills, K.A., Even, D. and Murray, J.C. (1992) Tetranucleotide repeat polymorphism at the human alpha fibrinogen locus (FGA). Human Molecular Genetics, 1, 779.

TH01 Polymeropoulos, M.H., Xiao, H., Rath, D.S. and Merril, C.R. (1991)

Tetranucleotide repeat polymorphism at the human tyrosine hydroxylase gene (TH). Nucleic Acids Research, 19, 3753.

TPOX Anker, R., Steinbrueck, T. and Donis-Keller, H. (1992) Tetranucleotide repeat polymorphism at the human thyroid peroxidase (hTPO) locus. Human Molecular Genetics, 1, 137.

VWA Kimpton, C.P., Walton, A. and Gill, P. (1992) A further tetranucleotide repeat polymorphism in the vWF gene. Human Molecular Genetics, 1, 287.

D3S1358 Li, H., Schmidt, L., Wei, M.-H., Hustad, T., Lerman, M.I., Zbar, B. and Tory, K.

(1993) Three tetranucleotide polymorphisms for loci: D3S1352, D3S1358, D3S1359. Human Molecular Genetics, 2, 1327.

D5S818 Cooperative Human Linkage Center GATA3F03.512

D7S820 Cooperative Human Linkage Center GATA3F01.511

D8S1179 Cooperative Human Linkage Center GATA7G07.37564

D13S317 Cooperative Human Linkage Center GATA7G10.415

D16S539 Cooperative Human Linkage Center GATA11C06.715

D18S51 Staub, R.E., Speer, M.C., Luo, Y., Rojas, K., Overhauser, J., Otto, L. and Gilliam, T.C. (1993) A microsatellite genetic linkage map of human chromosome 18. Genomics, 15, 48-56.

D21S11 Sharma, V. and Litt, M. (1992) Tetranucleotide repeat polymorphism at the D21S11 locus. Human Molecular Genetics, 1, 67.

Table 5.1 Original reference describing each of the 13 CODIS STR loci and the gender identification marker amelogenin.

Amelogenin Sullivan, K.M., Mannucci, A., Kimpton, C.P. and Gill, P. (1993) A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. BioTechniques, 15, 637-641.

Cooperative Human Linkage Center information is available via the Internet: http://www.chlc.org

Locus Name

Chromosomal Location

Physical Positiona

Repeat Motif ISFG Formatb

GenBank Accession c

GenBank Allele

Allele Range d

Number of Alleles Seene

c-fms proto-oncogene, 6th intron

Chr 5 149.484Mb

TAGA

X14720

12

5-16

20

alpha fibrinogen, 3rd intron

Chr 4 156.086 Mb

CTTT

M64982

21

12.2-51.2

80

tyrosine hydroxylase, 1st intron

Chr 11 2.156Mb

TCAT

D00269

9

3-14

20

thyroid peroxidase, 10th intron

Chr 2 1.436 Mb

GAAT

M68651

11

4-16

15

von Willebrand Factor, 40th intron

Chr 12 19.826Mb

[TCTG][TCTA]

M25858

18

10-25

28

D3S1358

3p21.31

Chr 3 45.543 Mb

[TCTG][TCTA]

NT_005997

18

8-21

24

D5S818

5q23.2

Chr 5 123.187Mb

AGAT

G08446

11

7-18

15

D7S820

7q21.11

Chr 7 83.401 Mb

GATA

G08616

12

5-16

30

D8S1179

8q24.13

Chr 8 125.863 Mb

[TCTA][TCTG]

G08710

12

7-20

17

D13S317

13q31.1

Chr 13 80.52 Mb

TATC

G09017

13

5-16

17

D16S539

16q24.1

Chr 16 86.168Mb

GATA

G07925

11

5-16

19

D18S51

18q21.33

Chr 18 59.098Mb

AGAA

L18333

13

7-39.2

51

D21S11

21q21.1

Chr 21 19.476Mb

Complex [TCTA][TCTG]

AP000433

29

12-41.2

82

aPhysical positions and chromosomal locations determined on July 2003 human genome reference sequence (NCBI build 34) using hgBLAT (http://genome.ucsc.edu).

bThe DNA Commission of the International Society of Forensic Genetics (ISFG) has published several papers encouraging standardization in STR allele nomenclature (see Bar et al. 1994, 1997). STR repeats should be called on the strand sequence originally described in the first public database entry using the first 5'-nucleotides that can define a repeat motif.

cGenBank sequence information for a particular STR locus may be accessed at (http://www.ncbi.nlm.nih.gov/GenBank) by entering the accession number shown here. Reference sequences are also available at http://www.cstl.nist.gov/biotech/strbase/seq_ref.htm.

dNumbers in this column refer to the number of repeat units present in the alleles. More detail on alleles that have been observed and their PCR products with commercially available STR kits may be found in Appendix I. eSee Appendix I.

location, the repeat motif, allele range, and GenBank accession number where the DNA sequence for a reference allele may be found. The chromosomal locations for these STRs have been updated on the recently completed human genome reference sequence. We have included detailed allele sequence information and PCR product sizes with commercially available STR kits in Appendix I.

Using the previously described classification scheme for categorizing STR repeat motifs (Urquhart et al. 1994), the 13 CODIS core STR loci may be divided up into four categories:

Table 5.2 (facing) Summary information on the 13 CODIS core STR loci.

1. Simple repeats consisting of one repeating sequence: TPOX, CSF1PO, D5S818, D13S317, D16S539;

2. Simple repeats with non-consensus alleles (e.g., 9.3): TH01, D18S51, D7S820;

3. Compound repeats with non-consensus alleles: VWA, FGA, D3S1358, D8S1179;

4. Complex repeats: D21S11.

COMMERCIALLY AVAILABLE STR KITS

A number of kits are available for single or multiplex PCR amplification of STR markers used in DNA typing. Two primary vendors for STR kits used by the forensic DNA community exist: the Promega Corporation located in Madison, Wisconsin, and Applied Biosystems located in Foster City, California. These companies have expended a great deal of effort over the past decade to bring STR markers to forensic scientists in kit form. More recently in Europe, companies such as Serac (Bad Homburg, Germany) and Biotype (Dresden, Germany) have begun offering commercial STR kits.

The technology has evolved quickly in the late 1990s for more sensitive, rapid, and accurate measurements of STR alleles. At the same time, the number of STRs that can be simultaneously amplified has increased from three or four with silver-stained systems to over 15 STRs using multiple-color fluorescent tags (see Chapter 13). A list of commercially available STR multiplexes and when they were released as products is shown in Table 5.3.

Table 5.3 (below)

Information on commercially available STR multiplexes (fluorescently-labeled).

Name

Source

Release Date STR Loci Included

TH01, TPOX, CSF1PO monoplexes (silver stain)

AmpF/STR® Blue

AmpF/STR® Green I

CTTv

Promega Feb 1993 TH01, TPOX, CSF1PO

Applied Oct 1996

Biosystems

Applied Jan 1997

Biosystems

Promega

Jan 1997

D3S1358, VWA, FGA Amelogenin, TH01, TPOX, CSF1PO CSF1PO, TPOX, TH01, VWA (vWF)

Name

Source

Release Date STR Loci Included

FFFL

GammaSTR PowerPlex™

AmpF/STR® Profiler Plus™

PowerPlex® 2.1

(for Hitachi FMBIO users)

PowerPlex® 16

PowerPlex® 16 BIO (for Hitachi FMBIO users)

AmpF/STR® Identifiler™

Promega Promega Promega

Applied Biosystems

Applied Biosystems

Applied Biosystems

Applied Biosystems

Promega

Promega

Promega

Applied Biosystems

AmpF/STR® Profiler Plus™ ID Applied (extra unlabeled D8-R primer) Biosystems

PowerPlex® ES

Promega

Applied Biosystems

Jan 1997 F13A1, FES/FPS, F13B, LPL

Jan 1997 D16S539, D13S317, D7S820, D5S818

Jan 1997 CSF1PO, TPOX, TH01, VWA, D16S539,

Sept 1998 D13S317, D7S820, D5S818

May 1997 D3S1358, VWA, FGA, Amelogenin, TH01,

TPOX, CSF1PO, D5S818, D13S317, D7S820

Dec 1997 D3S1358, VWA, FGA, Amelogenin, D8S1179,

D21S11, D18S51, D5S818, D13S317, D7S820

May 1998 D3S1358, D16S539, Amelogenin, TH01,

TPOX, CSF1PO, D7S820

Feb 1999 D3S1358, VWA, D16S539, D2S1338, Amelogenin,

D8S1179, D21S11, D18S51, D19S433, TH01, FGA

June 1999 D3S1358, TH01, D21S11, D18S51, VWA,

D8S1179, TPOX, FGA, Penta E

May 2000 CSF1PO, FGA, TPOX, TH01, VWA, D3S1358,

D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, Penta D, Penta E, amelogenin

May 2001 CSF1PO, FGA, TPOX, TH01, VWA, D3S1358,

D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, Penta D, Penta E, amelogenin

July 2001 CSF1PO, FGA, TPOX, TH01, VWA, D3S1358,

D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D2S1338, D19S433, amelogenin

Sept 2001 D3S1358, VWA, FGA, Amelogenin, D8S1179,

D21S11, D18S51, D5S818, D13S317, D7S820

Mar 2002 FGA, TH01, VWA, D3S1358, D8S1179, D18S51,

D21S11, SE33, amelogenin

Sept 2002 FGA, TH01, VWA, D3S1358, D8S1179, D16S539,

D18S51, D21S11, D2S1338, D19S433, SE33, amelogenin

Table 5.3 The adoption of the 13 core loci for CODIS in the United States has led to

(Continued) development of STR multiplexes that cover these markers. At the turn of the century, two PCR reactions were required to obtain information from all the 13 STRs: either PowerPlex® 1.1 and PowerPlex® 2.1 or Profiler Plus™ and COfiler™ (see Table 5.3). As an internal check to reduce the possibility of mixing up samples, both manufacturers included overlapping loci in their kits that should produce concordant data between samples amplified from the same biological material. The Profiler Plus™ and COfiler™ kits have the loci

PCR product size (bp)

100

150

200

250

300

350

400

PowerPlex® 16 kit (Promega Corporation)

PowerPlex® 16 kit (Promega Corporation)

TMR (Yellow) AMEL CXR (Red)

D3S1358 IHD1 D21S11 D18S51 [_Pentf_E_J

D5S818 D13S317 D7S82D D16S539 CSF1PO l_Penta_D VWA D8S1179 IPOX FGA

ILS600 CXR size standard

6-FAM (Blue) VIC (Green) NED (Yellow) PET (Red) LIZ (Orange)

AmpF/STR® Identifier™ kit (Applied Biosystems)

D8S1179 D21S11 D7S820 CSF1PO D3S1358 TH01 D13S317 D16S539 ¡^2S1_3_38J [~D19S433] VWA TPOX D18S51

AMEL D5S818 FGA

GS500 LIZ size standard

Figure 5.4

Commercially available STR kit solutions for a single amplification of the 13 CODIS core loci. General size ranges and dye-labeling strategies are indicated. The PowerPlex 16 kit uses four dyes while the Identifiler kit uses five dyes. Loci with dotted boxes are additional loci specific to each kit.

D3S1358 and D7S820 in common while the PowerPlex® 1.1 and PowerPlex® 2.1 have the loci TH01, TPOX, and VWA in common.

Since 2000, both Promega and Applied Biosystems have marketed multiplex PCR reactions that permit co-amplification of all 13 STRs in a single reaction along with the amelogenin sex-typing marker and two additional STR loci (Figure 5.4). Electropherograms with size separated PCR products for Promega's PowerPlex® 16 (Figure 5.5) can be viewed as color separated panels of loci or as an overlay of all colors. The allelic ladders for the Applied Biosystems' AmpFlSTR® Identifiler™ kits are displayed in Figure 5.6.

As will be discussed in the Technology section, two primary methods are used in modern forensic DNA laboratories to separate and detect fluorescently labeled STR alleles. Some PowerPlex kits have been balanced to work with the Hitachi FMBIO II scanner while PowerPlex® 16, Identifiler™, Profiler Plus™, and COfiler™ reactions are typically analyzed on an ABI Prism 310 or 3100 Genetic Analyzer capillary electrophoresis system (see Chapter 14).

Commercial manufacturers of STR kits have spent a great deal of research effort defining which markers would be included in each kit as well as verifying if primer pairs are compatible and will work well in combination with each other during multiplex PCR conditions (Wallin et al. 2002, Krenke et al. 2002). Promega has published and patented their PCR primer sequences (Masibay et al. 2000, Krenke et al. 2002) whereas Applied Biosystems have kept their primer m

WO 1» 1M 17» «4 I» MO 171 JOO JM Mi J7S «È Jtt till 4M «0

o blue panel

WO 1» 1M 17» «4 I» MO 171 JOO JM Mi J7S «È Jtt till 4M «0

D3S1358

TH01

D21S11

D18S51

Penta E

JLLJL

blue panel

yellow panel

VWA Amelogenin (sex-typing) :

D8S1179

TPOX

yellow panel

ILS600 DNA sizing standard red panel 500 bp

100 bp 200 bp 300 bp 400 bp

225 250 275 325 350 375 425 450 475

120 140 160 180 | 225 250 275

Figure 5.5

PowerPlex® 16 result from 1 ng genomic DNA.

sequences proprietary although some information has been revealed regarding the use of degenerate primers (see Chapter 6). The issue over failure to disclose kit primer sequences impacted several court cases early on in the legal acceptance of STR technology but appears to have been resolved now (D.N.A. Box 5.2).

Most laboratories do not have the time or resources to design primers, optimize PCR multiplexes, and quality control primer synthesis. The convenience of using ready-made kits is also augmented by the fact that widely used primer sets and conditions allow improved opportunities for sharing data between laboratories without fear of possible null alleles (see Chapter 6). Available STR multiplex sets vary based on which STR loci are included, the fluorescent dye combinations, the DNA strand that is labeled, allelic ladders present in kits, and most importantly, the primer sequences utilized for PCR amplification. It is important to keep in mind that commercially available kits quickly dictate which STRs will be used by the vast majority of forensic laboratories.

During the early adoption of STR typing technology in U.S. court systems, three cases ruled that DNA results would not be permissible as evidence because the commercial STR kit PCR primer sequences and developmental validation studies were not public information. These cases were People v. Bokin (San Francisco, California, May 1999), People v. Shreck (Boulder, Colorado, April 2000), and State v. Pfenning (Grand Isle, Vermont, Apr 2000).

Shortly after the Pfenning case, the Promega Corporation made the decision to publish their STR kit primer sequences (see news in Nature 27 July 2000 issue, volume 406, p. 336) and have done so since (Masibay et al. 2001, Krenke et al. 2002), along with obtaining several patents in the area of multiplex amplification of STR loci.

Applied Biosystems has repeatedly refused to release the primer sequences present in their STR kits claiming that this information is proprietary. The company is concerned that they would lose revenue if generic brand products were produced by other entities using the revealed primer information. However, in at least 16 cases, the primer sequences for the ProfilerPlus™ and COfiler™ kits have been supplied by Applied Biosystems under a protective court order. Numerous publications since 2000 have demonstrated the reliable use of Applied Biosystems STR kits including detailed validation studies (see Holt et al. 2002).

The arguments that not enough information exists to support the reliable use of commercial STR kits whose every component is not public knowledge have fallen by the wayside as millions of DNA profiles have been reliably generated with these kits in the past few years.

For further information:

Masibay, A. et al. (2000) Promega Corporation reveals primer sequences in its testing kits [letter]. Journal of Forensic Sciences, 45, 1360-1362. Krenke, BE. et al. (2002) Validation of a 16-locus fluorescent multiplex system.

Journal of Forensic Science, 47, 773-785. Holt, CL. et al. (2002) TWGDAM validation of AmpFlSTR PCR amplification kits for forensic DNA casework. Journal of Forensic Science, 47, 66-96. http://www.scientific.org/archive/archive.html

http://www.denverda.org/html_website/denver_da/DNA_resources.html http://www.denverda.org/legalResource/AB Sequence case list.pdf

D.N.A. Box 5.2 Disclosure of STR kit primer sequences

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Responses

  • nicole beck
    How codis core loci is determined?
    8 years ago
  • Aida
    What is codis fga tpox?
    7 years ago
  • Semret
    Do forensic scientists use 13 loci including gender loci?
    2 years ago
  • brigitte
    Where is 1320 codis loci at?
    1 year ago
  • Howard
    What is 13 codis STRS?
    7 months ago
  • isengrim noakes
    Do forensic scientists get health care?
    7 months ago
  • AARON
    What do the 13 core strs abbrevated?
    1 month ago
  • TIMOTHY BARR
    Why were the 13 core codis loci chosen?
    1 month ago

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