Forensic Science International
Volume 133, Issue 3 , Pages 220-227 , 5 May 2003

Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles

  • Craig Leibelt

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA
    • Corresponding Author InformationCorresponding author. Tel.: +1-650-554-2408; fax: +1-650-638-6393.
    • ,
  • Bruce Budowle

      Affiliations

    • Laboratory Division, FBI, 935 Pennsylvania Ave., NW, Washington, DC 20535, USA
    • ,
  • Patrick Collins

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA
    • ,
  • Yasser Daoudi

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA
    • ,
  • Tamyra Moretti

      Affiliations

    • Laboratory Division, FBI Academy, Quantico, VA 22135, USA
    • ,
  • Gary Nunn

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA
    • ,
  • Dennis Reeder

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA
    • ,
  • Rhonda Roby

      Affiliations

    • Applied Biosystems, 850 Lincoln Centre Drive, M/S 404-3, Foster City, CA 94404, USA

Received 25 October 2002 ,Revised 27 January 2003 ,Accepted 29 January 2003.

References 

  1. B. Budowle, T.R. Moretti, S.J. Niezgoda, B.L. Brown, CODIS and PCR-based short tandem repeat loci: law enforcement tools, in: Proceedings of the Second European Symposium on Human Identification, Promega Corporation, Madison, WI, 1998, pp. 73–88.
  2. Oldroyd NJ, Urquhart AJ, Kimpton CP, Millican ES, Watson SK, Downes T, et al. A highly discriminating octoplex short tandem repeat polymerase chain reaction system suitable for human individual identification. Electrophoresis. 1995;16:334–337
  3. Budowle B, Moretti TR, Baumstark AL, Defenbaugh DA, Keys KM. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, US Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians. Forensic Sci. 1999;44:1277–1286
  4. Budowle B, Masibay A, Anderson SJ, Barna C, Biega L, Brenneke S, et al. STR primer concordance study. Forensic Sci. Int. 2001;124:47–54
  5. Budowle B, Defenbaugh DA, Keys KM. Genetic cvariation at nine short tandem repeat loci in Chamorros and Filipinos from Guam. Legal Med. 2000;2:26–30
  6. Walsh PS, Varlaro J, Reynolds R. A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res. 1992;20:5061–5065
  7. 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;119:1–10
  8. AmpFℓSTR Identifiler User’s Manual, Version A, Applera Corporation, Foster City, 2001.
  9. P. Collins, L. Hennessy, C. Leibelt, R. Roby, D. Reeder, P. Foxall, 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. (2003) (accepted).
  10. Kline MC, Jenkins B, Rodgers S. Non-amplification of a vWA allele. J. Forensic Sci. 1998;43:250
  11. Walsh S, Kline MC, Jenkins B, Rodgers S. Non-amplification of a vWA allele. J. Forensic Sci. 1998;43:1103–1104
  12. Budowle B. STR allele concordance between different primer sets—a brief summary. Profiles DNA. 2000;3:10–11
  13. Budowle B, Sprecher CJ. Concordance study on population database samples using the PowerPlex™ 16 kit and AmpFℓSTR® Profiler Plus™ kit and AmpFℓSTR® Cofiler™ kit. J. Forensic Sci. 2001;46:637–641
  14. Wallin J, Holt C, Lazaruk K, Nguyen T, Walsh PS. Constructing universal multiplex PCR systems for comparative genotyping. J. Forensic Sci. 2002;47:1–14
  15. M.S. Nelson, E.N. Levedakou, J.R. Matthews, B.E. Early, D.A. Freeman, C.A. Kuhn, C.J. Sprecher, A.S. Amin, K.C. McElfresh, J.W. Schumm, Detection of a primer-binding site polymorphism for the STR locus D16S539 using the Poerplex® 1.1 system and validation of a degenerate primer to correct for the polymorphism, J. Forensic Sci. 47 (2002) 345–349.
  16. Gusmao L, Amorim A, Prata MJ, Pereira L, Lareu MV, Carracedo A. Failed PCR amplification of MBP-STR alleles due to polymorphism in the primer annealing region. Int. J. Legal Med. 1996;108:313–315
  17. Han GR, Song ES, Hwang JJ. Non-amplification of an allele of the D8S1179 locus due to a point mutation. Int. J. Legal Med. 2001;115:45–47
  18. C. Alves, L. Gusmao, L. Pereira, A. Amorim, Multiplex STR genotyping: comparison study, population data and new sequence information, in: Proceedings of the 19th International Congress of the International Society for Forensic Genetics, Munster, Germany, 2001, p. 67.
  19. Quality assurance standards for forensic DNA testing laboratories, DNA Advisory Board, Federal Bureau of Investigation, US Department of Justice, 1998.
  20. Peyret N, Seneviratne PA, Allawi HT, SantaLucia J. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G, and T·T mismatches. Biochemistry. 1999;38:3468–3477
  21. Hatim AT, SantaLucia J. Nearest-neighbor thermodynamics of Internal A·C mismatches in DNA: sequence dependence and pH effects. Biochemistry. 1998;37:9435–9444
  22. Hatim AT, SantaLucia J. Thermodynamics and NMR of internal G·T mismatches in DNA. Biochemistry. 1997;36:10581–10594
  23. Williams JF. Optimization strategies for the polymerase chain reaction. BioTechniques. 1989;7:762–768
  24. Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis. 1999;20:1682–1689

PII: S0379-0738(03)00035-5

doi: 10.1016/S0379-0738(03)00035-5

Forensic Science International
Volume 133, Issue 3 , Pages 220-227 , 5 May 2003

Article Tools

* Image Usage & Resolution