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Human identity testing with PCR-based systems

Abstract

Large numbers of repetitive stretches of DNA are present within the human genome that are associated with human individuality due to their polymorphic character. Approximately one-third of these repeat sequences is arranged as microsatellites or short tandem repeats (STRs) whose valuable application as state-of-the-art technique in human identity testing will be briefly summarized in this review. Prerequisties for successful DNA typing using STRs amplified by polymerase chain reaction (PCR) are outlined and particular attention is paid to the molecular structure of STRs from autosomes as well as from the Y chromosome. A comprehensive overview about current and emerging methods of STR analysis is given as well.

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References

  1. Edwards, A., Civitello, A., Hammond, 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 

  2. Brinkmann, B. (1996) The STR approach, in Advances in Forensic Haemogenetics, vol. 6, Springer-Verlag, Berlin, Heidelberg, New York, pp. 41–51.

    Google Scholar 

  3. Brinkmann, B., Möller, A., and Wiegand, P. (1995) Structure of new mutations in 2 STR systems. Int. J. Legal Med. 107, 201–203.

    PubMed  Article  CAS  Google Scholar 

  4. Brinkmann, B., Klintschar, M., Neuhuber, F., Hühne, J., and Rolf, B. (1998) Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62, 1408–1415.

    PubMed  Article  CAS  Google Scholar 

  5. Skowasch, K. and Brinkmann, B. (1992) optimized amplification of the polymorphic system Col2A1. Int. J. Legal Med. 105, 185–187.

    PubMed  Article  CAS  Google Scholar 

  6. Sambrock, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

  7. Budowle, B. and Baechtel, F. S. (1990) Modifications to improve the effectiveness of restriction fragment length polymorphism typing. Appl. Theor. Electrophor. 1, 181–187.

    PubMed  CAS  Google Scholar 

  8. Grimberg, J., Nawoschick, S., Belluscio, L., McKee, R., Tirck, A., and Eisenberg, A. (1989) A simple and efficient nonorganic procedure for the isolation of genomic DNA from blood. Nucleic Acids Res. 17, 8390.

    PubMed  Article  CAS  Google Scholar 

  9. Walsh, P. S., Metzger, D. A., and Higuchi, R. (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing of forensic material. Biotechniques 10, 506–513.

    PubMed  CAS  Google Scholar 

  10. Greenspoon, S. A., Scarpetta, M. A., Drayton, M. L., and Turek, S. A. (1998) Q1Aamp spin columns as a method of DNA isolation for forensic casework. J. Forensic Sci. 43, 1024–1030.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  12. Singer-Sam, J., Tanguay, R. L., and Riggs, A. D. (1989) Use of Chelex to improve the PCR signals from a small number of cells. Amplifications: A Forum for PCR Users, 3, 11.

    Google Scholar 

  13. Gill, P., Jeffreys, A. J., and Werrett, D. J. (1985) Forensic applications of DNA “fingerprints”. Nature 318, 577–579.

    PubMed  Article  CAS  Google Scholar 

  14. Wiegand, P., Schürenkamp, M., and Schütte, U. (1992) DNA extraction from mixtures of body fluid using mild preferential lysis. Int. J. Legal Med. 104, 359–360.

    PubMed  Article  CAS  Google Scholar 

  15. Wiegand, P., Madeja, M., and Brinkmann, B. (1994) Investigations on vaginal cell/sperm mixtures from microscopical slides, in Advances in Forensic Haemogenetics, vol. 5. (Bär, W., Fiori, A., and Rossi, U., eds.) Springer, Berlin Heidelberg New York, pp. 256–258.

    Google Scholar 

  16. DNA recommendations — 1994 report concerning further recommendations of the DNA commission of the ISFH regarding PCR-based polymorphisms in STR (short tandem repeat) systems. Int. J. Legal Med. 107, 159–160.

    Google Scholar 

  17. Considerations from the European DNA profiling group (EDNAP) concerning STR nomenclature. (1997) Eorensic Sci. Int. 87, 185–192.

    Article  Google Scholar 

  18. Urquhart, A., Kimpton, C. P., Downes, T. J., and Gill, P. (1994) Variation in short tandem repeat sequences—a survey of twelve microsatellite loci for use as forensic identification markers. Int. J. Legal Med. 107, 13–20.

    PubMed  Article  CAS  Google Scholar 

  19. Möller, A., Meyer, E., and Brinkmann, B. (1994) Different types of structural variation in STRs: HumFES/FPS, HumVWA and HumD21S11. Int. J. Legal Med. 106, 319–323.

    PubMed  Article  Google Scholar 

  20. Barber, M. D., Piercy, R. C., Anderson, J. F., and Parkin, B. H. (1995) Structural variation of novel alleles at the HumVWA and HumFES/FPS short tandem repeat loci. Int. J. Legal Med. 108, 31–35.

    PubMed  Article  CAS  Google Scholar 

  21. Dean, M., Lucas-Derse, S., Bolos, A., O’Brien, S. J., Kirkness, E. F., Fraser, C. M., and Goldman, D. (1991) Genetic mapping of the beta 1 GABA receptor gene to human chromosome 4, using a tetranucleotide repeat polymorphism. Am. J. Hum. Genet. 49, 621–626.

    PubMed  CAS  Google Scholar 

  22. Möller, A. and Brinkmann, B. (1994) Locus ACTBP2 (SE33)—Sequencing data reveal considerable polymorphism. Int. J. Legal Med. 106, 262–267.

    PubMed  Article  Google Scholar 

  23. Rolf, B., Schürenkamp, M., Junge, A., and Brinkmann, B. (1997) Sequence polymorphism at the tetranucleotide repeat of the human beta-actin related pseudogene H-beta-Ac-psi-2 (ACTBP2) locus. Int. J. Legal Med. 110, 69–72.

    PubMed  Article  CAS  Google Scholar 

  24. Akane, A. (1998) Sex Determination by PCR Analysis of the X-Y Amelogenin Gene. Methods Mol. Biol. 98, 245–250.

    PubMed  CAS  Google Scholar 

  25. Forster, P., Kayser, M., Meyer, E., Roewer, L., Pfeiffer, H., Benkmann, H., and Brinkmann, B. (1998) Phylogenetic resolution of complex mutational features at Y-STR DYS390 in aboriginal Australians and Papuans. Mol. Biol. Evol. 15, 1108–1114.

    PubMed  CAS  Google Scholar 

  26. Jobling, M. A., Pandya, A., and Tyler-Smith, C. (1997) The Y chromosome in forensic analysis and paternity testing. Int. J. Legal Med. 110, 118–124.

    PubMed  Article  CAS  Google Scholar 

  27. Roewer, L., Arnemann, J., Spurr, N. K., Grzeschik, K.-H., and Epplen, J. T. (1992) Simple repeat sequences on the human Y chromosome. Hum. Genet. 89, 389–394.

    PubMed  Article  CAS  Google Scholar 

  28. de Knijff, P., Kayser, M., Caglià, A., Corach, D., Fretwell, N., Gehrig, C., Graziosi, G., Heidorn, F., Herrmann, S., Herzog, B., Hidding, M., Honda, K., Jobling, M., Krawczak, M., Leim, K., Mouser, S., Meyer, E., Oesterreich, W., Pandya, A., Parson, W., Penacino, G., Perez-Lezaun, A., Piccinini, A., Prinz, M., Schmitt, C., Schneider, P. M., Szibor, R., Teifel-Greding, J., Weichhold, G., and Roewer, L. (1997) Chromosome Y microsatellites: population genetic and evolutionary aspects. Int. J. Leg. Med. 103, 134–140.

    Article  Google Scholar 

  29. Kayser, M., Caglia, A., Corach, D., Fretwell, N., Gehrig, C., Graziosi, G., Heidorn, F., Herrmann, S., Herzog, B., Hidding, M., Honda, K., Jobling, M., Krawczak, M., Leim, K., Mouser, S., Meyer, E., Oesterreich, W., Pandya, A., Parson, W., Penacino, G., Perez-Lezaun, A., Piccinini, A., Prinz, M., Schmitt, C., Schneider, P. M., Szibor, R., Teifel-Greding, J., Weichhold, G., de Knijff, P., and Roewer, L. (1997) Evaluation of Y-chromosomal STRs: a multicenter study. Int. J. Legal. Med. 110, 125–133.

    PubMed  Article  CAS  Google Scholar 

  30. Brinkmann, C., Forster, P., Schürenkamp, M., Horst, J., Rolf, B., and Brinkmann, B. (1999) Human Y-chromosomal STR haplotypes in a Kurdish population sample. Int. J. Leg. Med. 112, 181–183.

    Article  CAS  Google Scholar 

  31. Rolf, B., Meyer, E., Brinkmann, B., and de Knijff, P. (1998) Polymorphism at the tetranucleotide repeat locus DYS389 in 10 populations reveals strong geographic clustering. Eur. J. Hum. Genet. 6, 583–588.

    PubMed  Article  CAS  Google Scholar 

  32. Prinz, M., Boll, K., Baum, H., and Shaler, B. (1997) Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci. Int. 85, 209–218.

    PubMed  Article  CAS  Google Scholar 

  33. Butler, J. M., and Levin, B. C. (1998) Forensic applications of mitochondrial DNA. Trends Biotechnol. 16, 158–162.

    PubMed  Article  CAS  Google Scholar 

  34. 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.

    PubMed  CAS  Article  Google Scholar 

  35. Schneider, H. R. and Rand, S. (1995) High-resolution vertical PAGE: an alternative electrophoretic system with multiple forensic applications. Int. J. Legal Med. 108, 276–279.

    Article  Google Scholar 

  36. Puers, C., Hammond, H. A., Jin, L., Caskey, C. T., and Schumm, J. W. (1993) Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01 (AATG)n and reassignment of alleles in population analysis by using a locus-specific allelic ladder. Am. J. Hum. Genet. 53, 953–958.

    PubMed  CAS  Google Scholar 

  37. Budowle, B., Chakraborty, R., Giusti, A. M., Eisenberg, A. J., and Allen, R. C. (1991) Analysis of the variable number of tandem repeat locus D1S80 by the polymerase chain reaction followed by high resolution polyacrylamide gel electrophoresis. Am. J. Hum. Genet. 48, 137–144.

    PubMed  CAS  Google Scholar 

  38. Butler, J. M. (1998) The Use of Capillary Electrophoresis in Genotyping STR Loci. Methods Mol. Biol. 98, 279–289.

    PubMed  CAS  Google Scholar 

  39. Butler, J. M., Li, J., Shaler, T. A., Monforte, J. A., and Becker, C. H. (1999) Reliable genotyping of short tandem repeat loci without an allelic ladder using time-of-flight mass spectrometry. Int. J. Legal Med. 112, 45–49.

    PubMed  Article  CAS  Google Scholar 

  40. Berkenkamp, S., Kirpekar, F., and Hillenkamp, F. (1998) Infrared MALDI mass spectrometry of large nucleic acids. Science 281, 260–262.

    PubMed  Article  CAS  Google Scholar 

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Correspondence to Bernd Brinkmann.

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Hohoff, C., Brinkmann, B. Human identity testing with PCR-based systems. Mol Biotechnol 13, 123–136 (1999). https://doi.org/10.1385/MB:13:2:123

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Index Entries

  • Short tandem repeats (STRs)
  • PCR
  • allelic ladders
  • forensic validation
  • individual identification
  • DNA typing
  • capillary electrophoresis
  • automated genetic analysis