Additional information and reprint requests:
Julio J. Mulero, Ph.D.
Applied Biosystems
850 Lincoln Centre Dr. MS 404-3
Foster City, CA 94404
E-mail: [email protected]

Oral presentation at the 17th International Symposium on Human Identification, Nashville, TN 2006. Some of the data are also presented in the MiniFiler^TM PCR Amplification Kit User Guide “Experiments and Results” section.

Read the full text

About

PDF

Tools

Share a link

Email
Wechat
Bluesky

Abstract

Abstract: DNA typing of degraded DNA samples can be a challenging task when using the current commercially available multiplex short tandem repeat (STR) analysis kits. However, the ability to type degraded DNA specimens improves by redesigning current STR marker amplicons such that smaller sized polymerase chain reaction (PCR) products are generated. In an effort to increase the amount of information derived from these types of DNA samples, the AmpFℓSTR^® MiniFiler™ PCR Amplification Kit has been developed. The kit contains reagents for the amplification of eight miniSTRs which are the largest sized loci in the AmpFℓSTR^® Identifiler^® PCR Amplification Kit (D7S820, D13S317, D16S539, D21S11, D2S1338, D18S51, CSF1PO, and FGA). Five of these STR loci (D16S539, D21S11, D2S1338, D18S51, and FGA) also are some of the largest loci in the AmpFℓSTR^® SGM Plus^® kit. This informative nine-locus multiplex, which includes the gender-identification locus Amelogenin, has been validated according to the FBI/National Standards and SWGDAM guidelines. Our results demonstrate significant performance improvements in models of DNA degradation, PCR inhibition, and nonprobative samples when compared to the AmpFℓSTR^® Identifiler^® and SGM Plus^® kits. These data support that the MiniFiler™ kit will increase the likelihood of obtaining additional STR information from forensic samples in situations in which standard STR chemistries fail to produce complete profiles.

References

1 Dixon LA, Dobbins AE, Pulker HK, Butler JM, Vallone PM, Coble MD, et al. Analysis of artificially degraded DNA using STRs and SNPs–results of a collaborative European (EDNAP) exercise. Forensic Sci Int 2006; 164(1): 33–44.
10.1016/j.forsciint.2005.11.011
CAS PubMed Web of Science® Google Scholar
2 Bender K, Schneider PM, Rittner C. Application of mtDNA sequence analysis in forensic casework for the identification of human remains. Forensic Sci Int 2000; 113(1–3): 103–7.
10.1016/S0379-0738(00)00223-1
CAS PubMed Web of Science® Google Scholar
3 Just RS, Irwin JA, O’Callaghan JE, Saunier JL, Coble MD, Vallone PM, et al. Toward increased utility of mtDNA in forensic identifications. Forensic Sci Int 2004; 146:(Suppl): 147–9.
10.1016/j.forsciint.2004.09.045
CAS PubMed Web of Science® Google Scholar
4 Whitaker JP, Cotton EA, Gill P. A comparison of the characteristics of profiles produced with the AMPFlSTR SGM Plus^® multiplex system for both standard and low copy number (LCN) STR DNA analysis. Forensic Sci Int 2000; 129(1): 25–34.
Web of Science® Google Scholar
5 Kloosterman AD, Kersbergen P. Efficacy and limits of genotyping low copy number (LCN) DNA samples by multiplex PCR of STR loci. J Soc Biol 2003; 197(4): 351–9.
10.1051/jbio/2003197040351
CAS PubMed Google Scholar
6 Gill P, Whitaker J, Flaxman C, Brown N, Buckleton J. An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci Int 2000; 112(1): 17–40.
10.1016/S0379-0738(00)00158-4
CAS PubMed Web of Science® Google Scholar
7 Wiegand P, Kleiber M. Less is more—length reduction of STR amplicons using redesigned primers. Int J Legal Med 2001; 114(4–5): 285–7.
10.1007/s004140000162
CAS PubMed Web of Science® Google Scholar
8 Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 2003; 48(5): 1054–64.
10.1520/JFS2003043
CAS PubMed Web of Science® Google Scholar
9 Drabek J, Chung DT, Butler JM, McCord BR. Concordance study between Miniplex assays and a commercial STR typing kit. J Forensic Sci 2004; 49(4): 859–60.
10.1520/JFS2004032
CAS PubMed Web of Science® Google Scholar
10 Chung DT, Drabek J, Opel KL, Butler JM, McCord BR. A study on the effects of degradation and template concentration on the amplification efficiency of the STR Miniplex primer sets. J Forensic Sci 2004; 49(4): 733–40.
10.1520/JFS2003269
CAS PubMed Web of Science® Google Scholar
11 Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci 2005; 50(1): 43–53.
10.1520/JFS2004216
CAS PubMed Web of Science® Google Scholar
12 Grubwieser P, Muhlmann R, Berger B, Niederstatter H, Pavlic M, Parson W. A new “miniSTR-multiplex” displaying reduced amplicon lengths for the analysis of degraded DNA. Int J Legal Med 2006; 120(2): 115–20.
10.1007/s00414-005-0013-6
CAS PubMed Web of Science® Google Scholar
13 Opel KL, Chung DT, Drabek J, Tatarek NE, Jantz LM, McCord BR. The application of miniplex primer sets in the analysis of degraded DNA from human skeletal remains. J Forensic Sci 2006; 51(2): 351–6.
10.1111/j.1556-4029.2006.00077.x
CAS PubMed Web of Science® Google Scholar
14 Tsukada K, Takayanagi K, Asamura H, Ota M, Fukushima H. Multiplex short tandem repeat typing in degraded samples using newly designed primers for the TH01, TPOX, CSF1PO, and vWA loci. Legal Med 2002; 4: 239–45.
10.1016/S1344-6223(02)00049-4
CAS PubMed Google Scholar
15 Hill CR, Kline MC, Mulero JJ, Lagace RE, Chang CW, Hennessy LK, et al. Concordance study between the AmpFlSTR MiniFiler™ PCR amplification kit and conventional STR typing kits. J Forensic Sci 2007; 52(4): 870–3.
10.1111/j.1556-4029.2007.00491.x
CAS PubMed Web of Science® Google Scholar
16 Quality assurance standards for forensic DNA testing laboratories. Forensic Sci Commun 2000; 2(3). Available at http://www.fbi.gov/hq/lab/fsc/backissu/july2000/codis2a.htm. Accessed on April 28, 2008.
Google Scholar
17 Revised Validation Guidelines-Scientific Working Group on DNA Analysis Methods (SWGDAM). Forensic Sci Commun 2004; 6(3). Available at http://www.fbi.gov/hq/lab/fsc/backissu/july2004/standards/2004_03_standards02.htm. Accessed on April 28, 2008.
Google Scholar
18 Applied Biosystems. AmpFℓSTR^® Identifiler™ PCR amplification kit user’s manual. Foster City, CA: Applied Biosystems, 2001.
Google Scholar
19 Applied Biosystems. AmpFℓSTR^® SGM Plus™ PCR amplification kit user’s manual. Foster City, CA: Applied Biosystems, 2001.
Google Scholar
20 Coticone SR, Oldroyd N, Philips H, Foxall P. Development of the AmpFℓSTR SEfiler PCR amplification kit: a new multiplex containing the highly discriminating ACTBP2 (SE33) locus. Int J Legal Med 2004; 118: 224–34.
10.1007/s00414-004-0459-y
PubMed Web of Science® Google Scholar
21 Collins PJ, Hennessy LK, Leibelt CS, Roby RK, Reeder DJ, Foxall PA. Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFℓSTR Identifiler^® PCR Amplification Kit. J Forensic Sci 2004; 49: 1265–77.
10.1520/JFS2002195
CAS PubMed Web of Science® Google Scholar
22 Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, et al. Development and validation of the AmpFℓSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci 2006; 51(1): 64–75.
10.1111/j.1556-4029.2005.00016.x
CAS PubMed Web of Science® Google Scholar
23 Grossman PD, Bloch W, Brinson E, Chang CC, Eggerding FA, Fung S, et al. High-density multiplex detection of nucleic acid sequences: oligonucleotide ligation assay and sequence-coded separation. Nucleic Acids Res 1994; 22: 4527–34.
10.1093/nar/22.21.4527
CAS PubMed Web of Science® Google Scholar
24 Baron H, Fung S, Aydin A, Bahring S, Luft FC, Schuster H. Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nat Biotechnol 1996; 14: 1279–82.
10.1038/nbt1096-1279
CAS PubMed Web of Science® Google Scholar
25 Applied Biosystems. AmpFℓSTR^® MiniFiler™ PCR amplification kit user guide. Foster City, CA: Applied Biosystems, 2006.
Google Scholar
26 Sensabaugh GF. Biochemical markers of individuality. In: R Saferstein, editor. Forensic science handbook. New York: Prentice-Hall, Inc, 338–415.
Google Scholar
27 Brownstein MJ, Carpten JD, Smith JR. Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. BioTechniques 1996; 20: 1004–6.
10.2144/96206st01
CAS PubMed Web of Science® Google Scholar
28 Walsh PS, Fildes NJ, Reynolds R. Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res 1996; 24: 2807–12.
10.1093/nar/24.14.2807
CAS PubMed Web of Science® Google Scholar
29 Mulero JJ, Chang CW, Hennessy LK. Characterization of the N + 3 stutter product in the trinucleotide repeat locus DYS392. J Forensic Sci 2006; 51(5): 1069–73.
10.1111/j.1556-4029.2006.00227.x
CAS PubMed Web of Science® Google Scholar
30 Viguera E, Canceill D, Ehrlich SD. In vitro replication slippage by DNA polymerases from thermophilic organisms. J Mol Biol 2001; 312(2): 323–33.
10.1006/jmbi.2001.4943
CAS PubMed Web of Science® Google Scholar
31 Lazaruk K, Wallin J, Holt C, Nguyen T, Walsh PS. Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing. Forensic Sci Int 2001; 119(1): 1–10.
10.1016/S0379-0738(00)00388-1
CAS PubMed Web of Science® Google Scholar
32 Akane A, Matsubara K, Nakamura H, Takahashi S, Kimura K. Identification of the heme compound copurified with deoxyribonucleic acid (DNA) from bloodstains, a major inhibitor of polymerase chain reaction (PCR) amplification. J Forensic Sci 1994; 39: 362–72.
10.1520/JFS13607J
CAS PubMed Web of Science® Google Scholar
33 Sutlovic D, Definis Gojanovic M, Andelinovic S, Gugic D, Primorac D. Taq polymerase reverses inhibition of quantitative real time polymerase chain reaction by humic acid. Croat Med J 2005; 46(4): 556–62.
PubMed Web of Science® Google Scholar

Citing Literature

Volume53, Issue4

July 2008

Pages 838-852

This article also appears in:

DNA Analysis in Degraded and Unusual Specimens

Development and Validation of the AmpFℓSTR^® MiniFiler^TM PCR Amplification Kit: A MiniSTR Multiplex for the Analysis of Degraded and/or PCR Inhibited DNA*

Abstract

References

Citing Literature

References

Information

About Wiley Online Library

Help & Support

Opportunities

Connect with Wiley

Development and Validation of the AmpFℓSTR® MiniFilerTM PCR Amplification Kit: A MiniSTR Multiplex for the Analysis of Degraded and/or PCR Inhibited DNA*

Abstract

References

Citing Literature

References

Related

Information

Development and Validation of the AmpFℓSTR^® MiniFiler^TM PCR Amplification Kit: A MiniSTR Multiplex for the Analysis of Degraded and/or PCR Inhibited DNA*