Skip to main content
SpringerLink
Log in
Book cover

Forensic DNA Profiling Protocols pp 155–171Cite as

Analysis of Amplified Fragment-Length Polymorphisms (VNTR/STR Loci) for Human Identity Testing

  • Protocol

  • 1840 Accesses

Part of the book series: Methods in Molecular Biology ((MIMB,volume 98))

Abstract

Highly polymorphic variable number tandem repeat (VNTR) loci have proven very useful for human DNA testing purposes (1-3). Initially, these variants were characterized by restriction fragment-length polymorphism (RFLP) analysis. Subsequently, the polymerase chain reaction (PCR) provided significant methodological improvements, particularly enhanced sensitivity and specificity (4). The PCR-based technology for detection of VNTR alleles has been termed amplified fragment-length polymorphism (AMP-FLP) analysis (5). AMP-FLP analysis already has proven useful for the detection of multiallelic profiles (6), D17S5 (7), the 3’ hypervariable region of the apolipoprotein B gene (8,9), and particularly D1S80 (5,10).

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Wyman, A. R. and White, R. (1980) A high polymorphic locus in human DNA. Proc. Natl. Acad. Sci. USA 77, 6754–6758.

    Article  PubMed  CAS  Google Scholar 

  2. Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985) Hypervariable minisatellite regions in human DNA. Nature 314, 67–73.

    Article  PubMed  CAS  Google Scholar 

  3. Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985) Individual-specific fingerprints of human DNA. Nature 316, 76–79.

    Article  PubMed  CAS  Google Scholar 

  4. Saiki, R. K., Scharf, S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., and Arnheim, N. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction analysis for diagnosis of sickle cell anemia. Science 230, 1350–1354.

    Article  PubMed  CAS  Google Scholar 

  5. Budowle, B., Chakraborty, R., Giusti, A. M., Eisenberg, A. J., and Allen, R. C. (1991) Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE. Am. J. Hum. Genet. 48, 137–144.

    PubMed  CAS  Google Scholar 

  6. Jeffreys, A. J., Wilson, V., Neumann, R., and Keyte, J. (1988) Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res. 16,10,953–10,971.

    Article  PubMed  CAS  Google Scholar 

  7. Horn, G. T., Richards, B., and Klinger, K. W. (1989) Amplification of a highly polymorphic VNTR segment by the polymerase chain reaction. Nucleic Acids Res. 17, 2140.

    Article  PubMed  CAS  Google Scholar 

  8. Boerwinkle, E., Xiong, W., Fourest, E., and Chan, L. (1989) Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction: application to the apolipoprotein B 3′ hypervariable region. Proc. Natl. Acad. Sci. USA 86,212–216.

    Article  PubMed  CAS  Google Scholar 

  9. Ludwig, E. H., Friedl, W., and McCarthy, B. J. (1989) High-resolution analysis of a hypervariable region in the human apolipoprotein B gene. Am. J. Hum. Genet. 48,458–464.

    Google Scholar 

  10. Kasai, K., Nakamura, Y., and White, R. (1990) Amplification of a variable number of tandem repeat (VNTR) locus (pMCT1 18) by the polymerase chain reaction (PCR) and its application to forensic science. J. Forensic Sci. 35,1196–1200.

    PubMed  CAS  Google Scholar 

  11. Edwards, A., Civitello, A., Hammon, H. A., and Caskey, C. T. (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet. 49, 746–756.

    PubMed  CAS  Google Scholar 

  12. Edwards, A., Hammond, H., Jin, L., Caskey, C. T., and Chakraborty, R. (1992) Genetic variation at five trimeric and tetrameric repeat loci in four human population groups. Genomics 12, 241–253.

    Article  PubMed  CAS  Google Scholar 

  13. Hochmeister, M. N., Jung, M. M., Budowle, B., Borer U. V., and Dirnhofer, R. (1994) Swiss population data on three tetrameric short tandem repeat loci—VWA, HUMTHO1, and F13A1—derived using multiplex PCR and laser fluorescence detection. Int. J. Leg. Med. 107, 34–36.

    Article  CAS  Google Scholar 

  14. Hochmeister, M. N., Budowle, B., Borer, U. V., and Dirnhofer, R. (1995) Swiss population data on three tetrameric short tandem repeat loci—HUMTHO1, TPOX, CSF1PO—derived using the GenePrint Triplex PCR Amplification Kit. Int. J. Legal Med. 107,246–249.

    Article  PubMed  CAS  Google Scholar 

  15. Huang, N. E., Schumm, J., and Budowle, B. (1995) Chinese population data on three tetrameric short tandem repeat loci—HUMTHO1, TPOX, AND CSF1PO— derived using multiplex PCR and manual typing. Forensic Sci. Int. 71,131–136.

    Article  PubMed  CAS  Google Scholar 

  16. Gill, P., Kimpton, C. P., and Sullivan, K. (1992) A rapid method for identifying fixed specimens by DNA profiling. Electrophoresis 13, 173–175.

    Article  PubMed  CAS  Google Scholar 

  17. Sullivan, K. M., Pop, S., Gill, P., and Robertson, J. M. (1992) Automated DNA profiling by fluorescent labeling of PCR products. PCR Meth. Appl. 2, 34–40.

    CAS  Google Scholar 

  18. GenePrint Fluorescent STR Systems—Technical Manual. (1994) Promega Corporation, Madison, WI.

    Google Scholar 

  19. Comey, C. T., Koons, B. W., Presley, K. W., Smerick, J. B., Sobieralski, C. A., Stanley, D. M., and Baechtel, F. S. (1994) DNA extraction strategies for amplified fragment length polymorphism analysis. J. Forensic Sci. 39,1254–1269.

    CAS  Google Scholar 

  20. Waye J. S., Presley, L., Budowle, B., Shutler, G. G., and Fourney, R. M. (1989) A simple method for quantifying human genomic DNA in forensic specimen extracts. Biotechniques 7, 852–855.

    Article  PubMed  CAS  Google Scholar 

  21. Giusti, A. M. and Budowle, B. (1995) Chemiluminescence-based detection system for human DNA quantitation and restriction fragment length polymorphism (RFLP) analysis. Appl. Theoret. Electrophor. 5, 89–98.

    CAS  Google Scholar 

  22. Budowle, B., Baechtel, F. S., Smerick, J. B., Presley, K. W., Giusti, A. M., Parsons, G., Alevy, M., and Chakraborty, R. (1995) D1S80 population data in African Americans, Caucasians, Southeastern Hispanics, Southwestern Hispanics, and Orientals. J. Forensic Sci. 40, 38–44.

    PubMed  CAS  Google Scholar 

  23. Budowle, B., Koons, B. W., Keys, K. M., and Smerick, J. B. (1996) Methods for typing the STR triplex CSF1PO, TPOX, and HUMTHO1 that enable compatibility among DNA typing laboratories, in Advances in Forensic Haemogenetics, vol. 6 (Carracedo, A., Brinkman B., and Bar, W., eds.), Springer-Verlag, Berlin, pp. 107–114.

    Google Scholar 

  24. Allen, R. C., Graves, G., and Budowle, B. (1989) Polymerase chain reaction amplification products separated on rehydratable polyacrylamide gels and stained with silver. Biotechniques 7, 736–744.

    Article  PubMed  CAS  Google Scholar 

  25. Allen, R. C. and Graves, G. M. (1990) Rehydratable gels: a potential reference standard support for electrophoresing PCR-amplified DNA. Bio/Technol. 8, 1288–1290.

    Article  CAS  Google Scholar 

  26. Budowle, B. and Allen, R. C. (1991) Discontinuous polyacrylamide gel electrophoresis of DNA fragments, in Methods in Molecular Biology, vol. 9: Protocols in Human Molecular Genetics (Mathew, C. G, ed.), Humana, Clifton, NJ, pp. 123–132.

    Chapter  Google Scholar 

  27. Allen, R. C., Budowle, B., and Reeder, D. J. (1993) Resolution of DNA in the presence of mobility modifying polar and nonpolar compounds by discontinuous electrophoresis on rehydratable polyacrylamide gels. Appl. Theoret. Electrophor. 3, 173–181.

    CAS  Google Scholar 

  28. Allen, R. C. and Goldberg, C. L. (1995) Forensic applications of gel electrophoresis. Am. Biotechnol. Lab. 13, 8–12.

    PubMed  CAS  Google Scholar 

  29. Hagelberg, E., Sykes, B., and Hedges, R. (1989) Ancient bone DNA amplified. Nature 342, 485.

    Article  PubMed  CAS  Google Scholar 

  30. Hochmeister, M. N., Budowle, B., Borer, U. V., Eggmann, U. T., Comey, C. T., and Dirnhofer, R. (1991) Typing of DNA extracted from compact bone tissue from human remains. J. Forensic Sci. 36,1649–1661.

    PubMed  CAS  Google Scholar 

  31. Rogan, P. K. and Salvo, J. (1990) Study of nucleic acids isolated from ancient remains. Yearbook Phys. Anthropol. 33,195–214.

    Article  Google Scholar 

  32. Budowle, B., Koons, B. W., and Errera, J. D. (1996) Multiplex amplification and typing procedure for the loci D1S80 and amelogenin. J. Forensic Sci. 41, 660–663.

    PubMed  CAS  Google Scholar 

  33. Akane, A., Seki, A., Shiono, H., Nakamura, H., Hasegawa, M., Kagawa, M., Matsubara, K., Nakahori, Y., Nagafuchi, S., and Nakagome, Y. (1992) Sex determination of forensic samples by dual PCR amplification of an X-Y homologous gene. Forensic Sci. Int. 52, 143–148.

    Article  PubMed  CAS  Google Scholar 

  34. Sullivan, K., 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, 636–642.

    PubMed  CAS  Google Scholar 

  35. Ornstein, L. and Davis, B. J. (1962) Disc Electrophoresis, Parts 1 and 2. Distillation Ind., Rochester, NY.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Forensic Science Research and Training Center, FBI Academy, FBI Laboratory, Quantico, VA

    Bruce Budowle

  2. Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC

    Robert C. Allen

Authors
  1. Bruce Budowle
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert C. Allen
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. University of London, UK

    Patrick J. Lincoln

  2. LGC, Teddington, UK

    Jim Thomson

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Budowle, B., Allen, R.C. (1998). Analysis of Amplified Fragment-Length Polymorphisms (VNTR/STR Loci) for Human Identity Testing. In: Lincoln, P.J., Thomson, J. (eds) Forensic DNA Profiling Protocols. Methods in Molecular Biology, vol 98. Humana Press. https://doi.org/10.1385/0-89603-443-7:155

Download citation

  • DOI: https://doi.org/10.1385/0-89603-443-7:155

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-443-3

  • Online ISBN: 978-1-59259-204-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation