Skip to main content

Molecular Analysis for Forensic Casework and Parentage Testing

  • Chapter
Molecular Diagnostics
  • 6053 Accesses

Abstract

Disciplines in forensic science have developed alongside and continue to be dependent on technological advances in the corresponding basic scientific disciplines. This is true with forensic medicine, toxicology, and chemistry but has become most evident with the advent of PCR (polymerase chain reaction) and molecular biology, a field that has rapidly made way for powerful DNA-based methodologies that can be easily used for human identification. Applications are wide ranging, from paternity/maternity establishment to determination of violent criminal offenders through forensic casework. The current molecular techniques employed in identity testing can be used to generate genetic profiles that are so rare (<1 in 360 billion) that some laboratories will state that identity has been demonstrated and an analyst can confidently report that a biological specimen originated only from a specific individual or his/her identical twin.

Over the last decade, the public has become more aware of the power of DNA typing. Several infamous identity cases have been covered extensively in the media, including the murder trial of O. J. Simpson, the President Clinton –Monica Lewinsky blue dress scandal, the identification of the remains of the tomb of the unknown soldier, the identification of the Romanoff family remains, and the identification of slave-born descendents of the third president of the United States, President Thomas Jefferson. Most recently, DNA identification techniques have been brought to the forefront because of the tremendous task of finding and identifying remains of the victims of the September 11, 2001 terrorist attacks. After the attacks, more than 20,000 total biological samples were recovered combined from the rubble of the World Trade Center, the soil at the site of the United Flight 93 crash in Somerset, PA, and from the American Airlines Flight 77 Pentagon crash site. Biological material recovered from the scenes consisted primarily of bone, teeth, and small samples of soft tissue, which ranged from fresh, to gangrenous, to carbonized. However, reference samples brought from family members included bloodstains, toothbrushes, hair, clothing items, and razors. In the case of this mass disaster, the role of DNA should not be understated —as of December 2002, of the total number of victim identifications made, approx 38% were made exclusively with DNA evidence. Additionally, an approx 40% of the identifications made were through the combined use of DNA along with a more traditional identification method (dental records, personal identifiers, forensic anthropology) (1). Many of these identifications were made from minute amounts of charred, highly degraded biological samples that might have otherwise not been properly identified and returned to the families.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Carson, A. E., Boyer, D., and Smith, B. Identification of the heroes of United Flight 93. Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology. Personal communication, 2003.

    Google Scholar 

  2. Parentage Testing Program Unit. Annual Report Summary for Testing in 2001. American Association of Blood Banks, Bethesda, MD, 2002.

    Google Scholar 

  3. Shutler, G. G., Gagnon, P., Verret, G., et al. Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case. J. Forensic Sci. 44:623–626, 1999.

    PubMed  CAS  Google Scholar 

  4. Branicki, W., Kupiec, T., and Pawlowski, R. Validation of cytochrome b sequence analysis as a method of species identification. J. Forensic Sci. 48:83–87, 2003.

    PubMed  CAS  Google Scholar 

  5. Miller Coyle, H., Ladd, C., Palmbach, T., and Lee, H. C. The Green Revolution: botanical contributions to forensics and drug enforcement. Croat. Med. J. 42:340–345, 2001.

    Google Scholar 

  6. Wells, J. D., Introna, F., Jr., Di Vella, G., Campobasso, C. P., Hayes, J., and Sperling, F. A. H. Human and insect mitochondrial DNA analysis from maggots. J. Forensic Sci. 46:685–687, 2001.

    PubMed  CAS  Google Scholar 

  7. Jeffreys, A. J., Wilson, V., and Thein, S. L. Hypervariable m ‘ in-isatellite’ regions in human DNA. Nature 314:67–73, 1985.

    Article  PubMed  CAS  Google Scholar 

  8. Jeffreys, A. J., Wilson, V., and Thein, S. L. Individual-specific f ‘in-gerprints’ of human DNA. Nature 316:76–79, 1985.

    Article  PubMed  CAS  Google Scholar 

  9. Klevan, L., Horton, L., Carlson, D. P., and Eisenberg, A. J. Chemiluminescent detection of DNA probes in forensic analysis. Electrophoresis 16:1553–1558, 1995.

    Article  PubMed  CAS  Google Scholar 

  10. Budowle, B., Baechtel, F. S., Comey, C. T., Giusti, A. M., and Klevan, L. Simple protocols for typing forensic biological evidence: chemiluminescent detection for human DNA quantitation and restriction fragment length polymorphism (RFLP) analyses and manual typing of polymerase chain reaction (PCR) amplified polymorphisms. Electrophoresis 16:1559–1567, 1995.

    Article  PubMed  CAS  Google Scholar 

  11. Blake, E., Mihalovich, J., Higuchi, R., Walsh, P. S., and Erlich, H. Polymerase chain reaction (PCR) amplification and human leukocyte antigen (HLA)-DQ alpha oligonucleotide typing on biological evidence samples: casework experiences. J. Forensic Sci. 37:700–726, 1992.

    PubMed  CAS  Google Scholar 

  12. Kawasaki, E., Saiki, R., and Erlich, H. Genetic analysis using poly-merase chain reaction-amplified DNA and immobilized oligonu-cleotide probes: reverse dot-blot typing. Methods Enzymol. 218:369–381, 1993.

    Article  PubMed  CAS  Google Scholar 

  13. Rudin, N. and Inman, K. An Introduction to Forensic DNA Analysis. CRC Press, Boca Raton, FL, 2001.

    Book  Google Scholar 

  14. Giroti, R. I., Biswas, R., and Mukherjee, K. Restriction fragment length polymorphism and polymerase chain reaction: HLA-DQA1 and polymarker analysis of blood samples from transfusion recipients. Am. J. Clin. Pathol. 118:382–387, 2002.

    Article  PubMed  CAS  Google Scholar 

  15. Butler, J. M. Forensic DNA Typing: Biology and Technology Behind STR Markers. Academic, San Diego, CA, 2001.

    Google Scholar 

  16. Kimpton, C., Fisher, D., Watson, S., et al. Evaluation of an automated DNA profiling system employing multiplex amplification of four tetrameric STR loci. Int. J. Legal Med. 106:302–311, 1994.

    Article  PubMed  CAS  Google Scholar 

  17. Hammond, H. A., Jin, L., Zhong, Y., Caskey, C. T., and Chakraborty, R. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am. J. Hum. Genet. 55:175–189, 1994.

    PubMed  CAS  Google Scholar 

  18. Kloosterman, A. D., Budowle, B., and Daselaar, P. PCR-amplifica-tion and detection of the human D1S80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis. Int. J. Legal Med. 105:257–264, 1993.

    Article  PubMed  CAS  Google Scholar 

  19. Fregeau, C. J. and Fourney, R. M. DNA typing with fluorescently tagged short tandem repeats: a sensitive and accurate approach to human identification. Biotechniques 15:100–119, 1993.

    PubMed  CAS  Google Scholar 

  20. Gill, P., Kimpton, C. P., Urquhart, A., et al. Automated short tandem repeat (STR) analysis in forensic caseworka — strategy for the future. Electrophoresis 16:1543–1552, 1995.

    Article  PubMed  CAS  Google Scholar 

  21. Gill, P. Role of short tandem repeat DNA in forensic casework in the UKp —ast, present, and future perspectives. Biotechniques 32:366– 385, 2002.

    PubMed  CAS  Google Scholar 

  22. DNA Advisory Board. Quality Assurance Standards for Forensic DNA Testing Laboratories. Forensic Sci. Commun. [online] 2, 2000.

    Google Scholar 

  23. DNA Advisory Board Quality Assurance Standards for Convicted Offender DNA Databasing Laboratories. Forensic Sci. Commun. [online] 2, 2000.

    Google Scholar 

  24. FBI Director. Quality Assurance Audit for Forensic DNA and Convicted Offender DNA Databasing Laboratories. Forensic Sci. Commun. [online] 3, 2001.

    Google Scholar 

  25. Laboratory Accreditation Board. Accredited Forensic Science Laboratories. American Society of Crime Laboratory Directors, Garner, NC, 2003.

    Google Scholar 

  26. DNA Accreditation NFSTC. Directory of Accredited Private DNA Laboratories. National Forensic Science Technology Center, Largo FL, 2003.

    Google Scholar 

  27. Polesky, H. F. Impact of molecular (DNA) testing on determination of parentage. Arch. Pathol. Lab Med. 123:1060–1062, 1999.

    PubMed  CAS  Google Scholar 

  28. Baird, M. L. Use of DNA identification for forensic and paternity analysis. J. Clin. Lab Anal. 10:350–358, 1996.

    Article  PubMed  CAS  Google Scholar 

  29. Parentage Testing Accreditation Program. AABB Accredited Parentage Testing Facilities. American Association of Blood Banks, Bethesda, MD, 2003.

    Google Scholar 

  30. Lee, H. C., Ladd, C., Scherczinger, C. A., and Bourke, M. T. Forensic applications of DNA typing: part 2: collection and preservation of DNA evidence. Am. J. Forensic Med. Patholol. 19:10–18, 1998.

    Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  33. Burgoyne, L. A. Solid medium and method for DNA storage. US Patent 5,496,562, 1996.

    Google Scholar 

  34. Krenke, B. E., Tereba, A., Anderson, S. J., et al. Validation of a 16-locus fluorescent multiplex system. J. Forensic Sci. 47:773–785, 2002.

    PubMed  CAS  Google Scholar 

  35. Burgoyne, L. A. Convenient DNA collection and processing: disposable toothbrushes and FTA paper as a non-threatening buccal-cell collection kit compatible with automatable DNA processing, in Proceedings of the Eighth International Symposium on Human Identification, Madison, WI, p. 153, 1997.

    Google Scholar 

  36. Scherczinger, C. A., Bourke, M. T., Ladd, C., and Lee, H. C. DNA extraction from liquid blood using QIAamp. J. Forensic Sci. 42:893– 896, 1997.

    PubMed  CAS  Google Scholar 

  37. Qiagen. QIAamp DNA Mini Kit and QIAamp DNA Blood Mini Kit Handbook. Qiagen. Valencia, CA, 2003.

    Google Scholar 

  38. Vandenberg, N. and van Oorschot, R. A. Extraction of human nuclear DNA from feces samples using the QIAamp DNA stool mini kit. J. Forensic Sci. 47:993–995, 2002.

    PubMed  CAS  Google Scholar 

  39. Sinclair, K. and McKechnie, V. M. DNA extraction from stamps and envelope flaps using QIAamp and QIAshredder. J. Forensic Sci. 45:229–230, 2000.

    PubMed  CAS  Google Scholar 

  40. Budowle, B., Smith, J. A. L., Moretti, T., and DiZinno, J. DNA Typing Protocols: Molecular Biology and Forensic Analysis. Biotechniques, Westborough, MA, 2000.

    Google Scholar 

  41. Budimlija, Z. M., Prinz, M. K., Zelson-Mundorff, A., et al. World Trade Center human identification project: experiences with individual body identification cases. Croat. Med. J. 44:259–263, 2003.

    PubMed  Google Scholar 

  42. Walsh, D. J., Corey, A. C., Cotton, R. W., et al. Isolation of deoxyri-bonucleic acid (DNA) from saliva and forensic sciences samples containing saliva. J. Forensic Sci. 37:387–395, 1992.

    PubMed  CAS  Google Scholar 

  43. Yoshida, K., Sekiguchi, K., Mizuno, N., et al. The modified method of two-step differential extraction of sperm and vaginal epithelial cell DNA from vaginal fluid mixed with semen. Forensic Sci. Int. 72:25–33, 1995.

    Article  PubMed  CAS  Google Scholar 

  44. Promega. DNA IQ SystemS —mall Sample Casework Protocol. Promega Corporation, Madison, WI, 2002.

    Google Scholar 

  45. Greenspoon, S. and Ban, J. Robotic extraction of mock sexual assault samples using the Biomek 2000 and the DNA IQ system. Profiles DNA 5:3–5, 2002.

    Google Scholar 

  46. Hopwood, A., Oldroyd, N., Fellows, S., Ward, R., Owen, S. A., and Sullivan, K. Rapid quantification of DNA samples extracted from buccal scrapes prior to DNA profiling. Biotechniques 23:18–20, 1997.

    PubMed  CAS  Google Scholar 

  47. Hopwood, A. J., Mannucci, A., and Sullivan, K. M. DNA typing from human faeces. Int. J. Legal Med. 108:237–243, 1996.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  49. Waye, J. S., Michaud, D., Bowen, J. H., and Fourney, R. M. Sensitive and specific quantification of human genomic deoxyri-bonucleic acid (DNA) in forensic science specimens: casework examples. J. Forensic Sci. 36:1198–1203, 1991.

    PubMed  CAS  Google Scholar 

  50. Walsh, P. S., Varlaro, J. and Reynolds, R. A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res. 20:5061–5065, 1992.

    Article  PubMed  CAS  Google Scholar 

  51. Fox, J. C., Cave, C. A., and Schumm, J. W. Development, characterization, and validation of a sensitive primate-specific quantification assay for forensic analysis. Biotechniques 34:314–322, 2003.

    PubMed  CAS  Google Scholar 

  52. Walker, J. A., Gail, K. E., Xing, J., Shewale, J., Sinha, S. K., and Batzer M. A. Human DNA quantitation using Alu element-based polymerase chain reaction. Anal. Biochem. 315:122–128, 2003.

    Article  PubMed  CAS  Google Scholar 

  53. Nicklas, J. A. and Buel, E. Development of an Alu-based, QSY 7-labeled primer PCR method for quantitation of human DNA in forensic scamples. J. Forensic Sci. 48:282–291, 2003.

    PubMed  CAS  Google Scholar 

  54. Sifis, M. E., Both, K., and Burgoyne, L. A. A more sensitive method for the quantitation of genomic DNA by Alu amplification. J. Forensic Sci. 47:589–592, 2002.

    PubMed  CAS  Google Scholar 

  55. Mandrekar, M. N., Erickson, A. M., Kopp, K., et al. Development of a human DNA quantitation system. Croat. Med. J. 42:336–339, 2001.

    PubMed  CAS  Google Scholar 

  56. Gill, P., Urquhart, A., Millican, E., et al. A new method of STR interpretation using inferential logic- development of a criminal intelligence database. Int. J. Legal Med. 109:14–22, 1996.

    Article  PubMed  CAS  Google Scholar 

  57. Chakraborty, R., Stivers, D.N., Su, B., Zhong, Y., and Budowle, B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 20:1682–1696, 1999.

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  59. Kimpton, C. P., Gill, P., Walton, A., Urquhart, A., Millican, E. S., and Adams, M. Automated DNA profiling employing multiplex amplification of short tandem repeat loci. PCR Methods Appl. 3:13–22, 1993.

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  61. Buel, E., Schwartz, M. B., and LaFountain, M. J. Capillary elec-trophoresis STR analysis: comparison to gel-based systems. J. Forensic Sci. 43:164–170, 1998.

    PubMed  CAS  Google Scholar 

  62. Ruitberg, C. M., Reeder, D. J., and Butler, J. M. STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res. 29:320–322, 2001.

    Article  PubMed  CAS  Google Scholar 

  63. Carey, L. and Mitnik, L. Trends in DNA forensic analysis. Electrophoresis 23:1386–1397, 2002.

    Article  PubMed  CAS  Google Scholar 

  64. Moretti, T. R., Baumstark, A. L., Defenbaugh, D. A., Keys, K. M., Smerick J. B., and Budowle, B. Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples. J. Forensic Sci. 46:647–660, 2001.

    PubMed  CAS  Google Scholar 

  65. Frazier, R. R., Millican, E. S., Watson, S. K., et al. Validation of the Applied Biosystems Prism 377 automated sequencer for the forensic short tandem repeat analysis. Electrophoresis 17:1550–1552, 1996.

    Article  PubMed  CAS  Google Scholar 

  66. Fregeau, C. J., Bowen, K. L., and Fourney, R. M. Validation of highly polymorphic fluorescent multiplex short tandem repeat systems using two generations of DNA sequencer. J. Forensic Sci. 44:133–166, 1999.

    PubMed  CAS  Google Scholar 

  67. Lazaruk, K., Walsh, P. S., Oaks, F., et al. Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument. Electrophoresis 19:86–93, 1998.

    Article  PubMed  CAS  Google Scholar 

  68. Moretti, T. R., Baumstark, A. L., Defenbaugh, D. A., Keys, K. M, Brown, A. L., and Budowle, B. Validation of STR typing by capillary electrophoresis. J. Forensic Sci. 46:661–676, 2001.

    PubMed  CAS  Google Scholar 

  69. Tomsey, C. S., Kurtz, M., Kist, F., Hockensmith, M., and Call, P. Comparison of PowerPlex 16, PowerPlex 1.1/2.1, and ABI AmpflSTR Profiler Plus/COfiler for forensic use. Croat. Med. J. 42:239–243, 2001.

    PubMed  CAS  Google Scholar 

  70. Sgueglia, J. B., Geiger, S., and Davis, J. Precision studies using the ABI Prism 3100 genetic analyzer for forensic DNA analysis. Anal. Bioanal. Chem. [online], 376:1247–1254, 2003.

    Article  PubMed  CAS  Google Scholar 

  71. Budowle, B., Masibay, A., Anderson, S. J., et al. STR primer concordance study. Forensic Sci. Int. 124:47–54, 2001.

    Article  PubMed  CAS  Google Scholar 

  72. Budowle, B. and Sprecher, C. J. Concordance study on population database samples using the PowerPlex 16 kit and AmpFlSTR Profiler Plus kit and AmpFlSTR COfiler kit. J. Forensic Sci. 46:637–641, 2001.

    PubMed  CAS  Google Scholar 

  73. Alves, C., Amorim, A., Gusmao, L., and Pereira L. VWA STR geno-typing: further inconsistencies between Perkin-Elmer and Promega kits. Int. J. Legal Med. 115:97–99, 2001.

    Article  PubMed  CAS  Google Scholar 

  74. Holland, M. M. and Parsons, T. J. Mitochondrial DNA sequence analysis —lidation and use for forensic casework. Forensic Sci. Rev. 11:22–50, 1999.

    Google Scholar 

  75. Butler, J. M. and Levin, B. C. Forensic applications of mitochondr-ial DNA. Trends Biotechnol. 16:158–162, 1998.

    Article  PubMed  CAS  Google Scholar 

  76. Anderson S., Bankier A. T., Barrell B. G., et al. Sequence and organization of the human mitochondrial genome. Nature 290:457–465, 1981.

    Article  PubMed  CAS  Google Scholar 

  77. Carracedo, A., D’Aloja, E., Dupuy, B., et al. Reproducibility of mtDNA analysis between laboratories: a report of the European DNA Profiling Group (EDNAP). Forensic Sci. Int. 97:165–170, 1998.

    Article  PubMed  CAS  Google Scholar 

  78. Wilson, M. R., DiZinno, J. A., Polanskey, D., Replogle, J., and Budowle, B. Validation of mitochondrial DNA sequencing for forensic casework analysis. Int. J. Legal Med. 108:68–74, 1985.

    Article  Google Scholar 

  79. Stewart, J. E., Aagaard, P. J., Pokorak, E. G., Polanskey, D., and Budowle, B. Evaluation of a multicapillary electrophoresis instrument for mitochondrial DNA typing. J. Forensic Sci. 48:571–580, 2003.

    PubMed  CAS  Google Scholar 

  80. Tully, G., Sullivan, K. M., Nixon, P., Stones, R. E., and Gill, P. Rapid detection of mitochondrial sequence polymorphisms using multiplex solid-phase fluorescent minisequencing. Genomics 34:107–113, 1996.

    Article  PubMed  CAS  Google Scholar 

  81. Gabriel, M. N., Huffine, E. F., Ryan, J. H., Holland, M. M., and Parsons, T. J. Improved mtDNA sequence analysis of forensic remains using a “mini-primer set ” amplification strategy. J. Forensic Sci. 46:247–253, 2001.

    PubMed  CAS  Google Scholar 

  82. Butler, J. M., Wilson, M. R., and Reeder, D. J. Rapid mitochondrial DNA typing using restriction enzyme digestion of polymerase chain reaction amplicons followed by capillary electrophoresis separation with laser-induced fluorescence detection. Electrophoresis 19:119–124, 1998.

    Article  PubMed  CAS  Google Scholar 

  83. LaBerge, G. S., Shelton, R. J., and Danielson, P. B. Forensic utility of DNA mitochondrial DNA analysis based on denaturing high-performance liquid chromatography. Croat. Med. J. 44:281–288, 2003.

    PubMed  Google Scholar 

  84. Gabriel, M. N., Calloway, C. D., Reynolds, R. L., and Primorac, D. Identification of human remains by immobilized sequence-specific oligonucleotide probe analysis of mtDNA hypervariable regions I and II. Croat. Med. J. 44:293–298, 2003.

    PubMed  Google Scholar 

  85. Ivanov, P. L., Wadhams, M. J., Roby, R. K., Holland, M. M., Weedn, V. W., and Parsons, T. J. Mitochondrial DNA sequence hetero-plasmy in the Grand Duke of Russia Georgij Ramanov establishes the authenticity of the remains of the Tsar Nicholas II. Nat. Genet. 12:417–420, 1996.

    Article  PubMed  CAS  Google Scholar 

  86. Grzybowski, T. Extremely high levels of human mitochondrial DNA heteroplasmy in single hair roots. Electrophoresis 21:548–553, 2000.

    Article  PubMed  CAS  Google Scholar 

  87. Scientific Working Group on DNA Analysis Methods (SWGDAM). Guidelines for mitochondrial DNA (mtDNA) nucleotide sequence interpretation. Forensic Sci. Commun. [online] 5, 2003.

    Google Scholar 

  88. Melton, T. and Nelson, K. Forensic mitochondrial DNA analysis: two years of commercial casework experience in the United States. Croat. Med. J. 42:298–303, 2001.

    PubMed  CAS  Google Scholar 

  89. Jobling, M. A. and Tyler-Smith, C. Fathers and sons: the Y chromosome and human evolution. Trends Genet. 11:449–456, 1995.

    Article  PubMed  CAS  Google Scholar 

  90. Foster, E. A., Jobling, M. A., Taylor, P. G., et al. Jefferson fathered slave’s last child. Nature 396:27–28, 1998.

    Article  PubMed  CAS  Google Scholar 

  91. Ciminelli, B. M., Pompei, F., Malaspina, P., et al. Recurrent simple tandem repeat mutations during human Y-chromosome radiation in Caucasian subpopulations. J. Mol. Evol. 41:966–973, 1995.

    Article  PubMed  CAS  Google Scholar 

  92. Kayser, M., Caglia, A., Corach, D., et al. Evaluation of Y-chromo-somal STRs: a multicenter study. Int. J. Legal Med. 110:125–133, 141–149, 1997.

    Article  CAS  Google Scholar 

  93. Perez-Lezaun, A., Calafell, F., Seielstad, M., et al. Population genetics of Y- c hromosome short tandem repeats in humans. J. Mol. Evol. 45:265–270, 1997.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  95. Redd, A. J., Clifford, S. L., and Stoneking, M. Multiplex DNA typing of short-tandem repeat loci on the Y chromosome. Biol. Chem. 378:923–927, 1997.

    Article  PubMed  CAS  Google Scholar 

  96. Prinz, M., Ishii, A., Coleman, A., Baum, H. J., and Shaler, R. C. Va lidation and casework application of a Y chromosome specific STR multiplex. Forensic Sci. Int. 120:177–188, 2001.

    Article  PubMed  CAS  Google Scholar 

  97. Gonzalez-Neira A., Elmoznino, M., Lareu, M. V., et al. Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies. Forensic Sci. Int. 122:19–26, 2001.

    Article  PubMed  CAS  Google Scholar 

  98. Bosch, E., Lee, A. C., Calafell, F., et al. High resolution Y chromosome typing: 19 STRs amplified in three multiplex reactions. Forensic Sci. Int. 125:42–51, 2002.

    Article  PubMed  CAS  Google Scholar 

  99. Butler, J. M., Schoske, R., V a llone, P. M., Kline, M. C., Redd, A. J., and Hammer, M. F. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci. Int. 129:10–24, 2002.

    Article  PubMed  CAS  Google Scholar 

  100. Sinha, S. K., Budowle, B., Arcot, S. S., et al. Development and validation of a multiplexed Y-chromosome STR genotyping system, Y-PLEX 6, for forensic casework. J. Forensic Sci. 48:93–103, 2003.

    PubMed  CAS  Google Scholar 

  101. Schoske, R., Vallone, P. M., Ruitberg, C. M., and Butler, J. M. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal. Bioanal. Chem. 375:333–343, 2003.

    PubMed  CAS  Google Scholar 

  102. Meng, C. Y., Both, K., and Burgoyne, L. A. Casework: A Y-STR triplex for use after autosomal multiplexes. Forensic Sci. Commun. [online] 5, 2003.

    Google Scholar 

  103. Hall, A. and Ballantyne, J. The development of an 18-locus Y-STR system for forensic casework. Anal. Bioanal. Chem. [online], 376: 1234–1246, 2003.

    Article  PubMed  CAS  Google Scholar 

  104. Sinha, S. K., Nasir, H., Gross, A. M., Budowle, B., and Shewale, J. G. Development and validation of the Y-PLEX 5, 1 Y-chromosome STR genotyping system, for forensic casework. J. Forensic Sci. 48:985–1000, 2003.

    PubMed  CAS  Google Scholar 

  105. Gusmao, L., Gonzalez-Neira, A., Pestoni, C., Brion, M., Lareu, M. V., and Carracedo, A. Robustness of the Y STRs DyS19, DYS389 I and II, DYS390 and DYS393: optimization of a PCR pentaplex. Forensic Sci. Int. 106:163–172, 1999.

    Article  PubMed  CAS  Google Scholar 

  106. Carracedo, A., Beckmann, A., Bengs, et al. Results of a collaborative studey of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DyS19, DYS389 I and II, DYS390, and DYS393 in a PCR pentaplex format. Forensic Sci. Int. 119:28–41, 2001.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  108. Prinz, M., Ishii, A., Coleman, A., Baum, H. J., and Shaler, R. C. Validation and casework application of a Y chromosome specific STR multiplex. Forensic Sci. Int. 120:177–188, 2001.

    Article  PubMed  CAS  Google Scholar 

  109. Dekairelle, A. F. and Hoste, B. Application of a Y-STR-pentaplex PCR (DYS19, DYS389I and II, DYS390 and DYS393 to sexual assault cases. Forensic Sci. Int. 118:122–125, 2001.

    Article  PubMed  CAS  Google Scholar 

  110. Gill, P., Brenner, C., Brinkmann, B., et al. DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. Forensic Sci. Int. 124:5–10, 2001.

    Article  PubMed  CAS  Google Scholar 

  111. National Institute of Justice. Solicitation for forensic DNA research and development for FY 2003. US Department of Justice, Office of Justice Programs. Washington, DC, 2003.

    Google Scholar 

  112. Lowe, A. L., Urquhart, A., Foreman, L. A., and Evett, I. W. Inferring ethnic origin by means of an STR profile. Forensic Sci. Int. 119:17–22, 2001.

    Article  PubMed  CAS  Google Scholar 

  113. Grimes, E. A., Noake, P. J., Dixon, L., and Urquhart, A. Sequence polymorphism in the human melanocortin 1 receptor gene as an indicator of the red hair phenotype. Forensic Sci. Int. 122:124–129, 2001.

    Article  PubMed  CAS  Google Scholar 

  114. Ayres, K. L., Chaseling, J., and Balding, D. J. Implications for DNA identification arising from an analysis of Australian forensic databases. Forensic Sci. Int. 129:90–98, 2002.

    Article  PubMed  CAS  Google Scholar 

  115. Associated Press. DNA test showing ancestry may have helped La. Search. USA Today, June 5, 2003.

    Google Scholar 

  116. Schneider, P. M, Seo, Y., and Rittner, C. Forensic mtDNA hair analysis excludes a dog from having caused a traffic accident. Int. J. Legal Med. 112:315–316, 1999.

    Article  PubMed  CAS  Google Scholar 

  117. Padar, Z., Angyal, M., Egyed, B., et al. Canine micosatellite polymorphisms as the resolution of an illegal animal death case in a Hungarian zoological gardens. Int. J. Legal Med. 115:79–81, 2001.

    Article  CAS  Google Scholar 

  118. Menotti-Raymond, M., David, V.A., Stephens, J. C., Lyons, L. A., and O’Brien, S. J. Genetic individualization of domestic cats using feline STR loci for forensic applications. J. Forensic Sci. 42:1039–1051, 1997.

    PubMed  CAS  Google Scholar 

  119. Padar, Z., Egyed, B., Kontadakis, K., et al. Canine STR analyses in forensic practice. Observation of a possible mutation in a dog hair. Int. J. Legal Med. 116:286–288, 2002.

    PubMed  CAS  Google Scholar 

  120. Butler, J. M., David, V., O’Brien, S., and Menotti-Raymond, M. The MeowPlex: a new DNA test using tetranucleotide STR markers for the domestic cat. Profiles DNA 5:7–10, 2002.

    Google Scholar 

  121. Menotti-Raymond, M., David, V., Wachter, L., Yuhki, N., and O’Brien, S. J. Quantitative polymerase chain reaction-based assay for estimating DNA yield extracted from domestic cat specimens. Croat. Med. J. 44:327–331, 2003.

    PubMed  Google Scholar 

  122. Savolainen, P., Arvestad, L., and Lundeberg, J. A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dog. J. Forensic Sci. 45:990–999, 2000.

    PubMed  CAS  Google Scholar 

  123. NDIS Statistics. Combined DNA Index System. June, 2003. Available at http://www.fbi.gov/hq/lab/codis/index1.htm.

  124. Chanock, S. Candidate genes and single nucleotide polymorphisms (SNPs) in the study of human disease. Dis. Markers 17:89–98, 2001.

    PubMed  CAS  Google Scholar 

  125. Botstein, D. and Risch, N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33(Suppl.):228–237, 2003.

    Article  PubMed  CAS  Google Scholar 

  126. Jobling, M. A. Y-Chromosomal SNP haplotype diversity in forensic analysis. Forensic Sci. Int. 118: 158–162, 2001.

    Article  PubMed  CAS  Google Scholar 

  127. Wang, D. G., Fan, J. B., Siao, C. J., et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082, 1998.

    Article  PubMed  CAS  Google Scholar 

  128. Heller, M. J. DNA microarray technology: devices. Annu. Rev. Biomed. Eng. 4:129–153, 2002.

    Article  PubMed  CAS  Google Scholar 

  129. Linacre, A. and Graham, D. Role of molecular diagnostics in forensic science. Expert Rev. Mol. Diagn. 2:346–353, 2002.

    Article  PubMed  CAS  Google Scholar 

  130. Salisbury, B. A., Pungliya, M., Choi, J. Y., Jiang, R., Sun, X. J., and Stephens, J. C. SNP and haplotype variation in the human genome. Mutat. Res. 526:53–61, 2003.

    PubMed  CAS  Google Scholar 

  131. Gill, P., Ivanov, P. L., Kimpton, C., et al. Identification of the remains of the Romanov family by DNA analysis. Nat. Genet. 6:130–135, 1994.

    Article  PubMed  CAS  Google Scholar 

  132. Strom, C. M. and Rechitsky, S. Use of nested PCR to identify charred human remains and minute amounts of blood. J. Forensic Sci. 43:696–700, 1998.

    PubMed  CAS  Google Scholar 

  133. Schmerer, W.M., Hummel, S., and Herrmann, B. Optimized DNA extraction to improve reproducibility of short tandem repeat geno-typing with highly degraded DNA as target. Electrophoresis 20:1712–1716, 1999.

    Article  PubMed  CAS  Google Scholar 

  134. Gill, P., Whitaker, J., Flaxman, C., Brown, N., and Buckleton, J. An investigation of the rigor of interpretation rules for STRs derived from less than 100 pg of DNA. Forensic Sci. Int. 112:17–40, 2000.

    Article  PubMed  CAS  Google Scholar 

  135. Whitaker, J. P., Cotton, E. A., and Gill, P. A comparison of the characteristics of profiles produced w ith t he AMPFlSTR SGM Plus multiplex system for both standard and low copy number (LCN) STR DNA analysis. Forensic Sci. Int. 123:215–223, 2001.

    Article  PubMed  CAS  Google Scholar 

  136. Gill, P. Application of low copy number DNA profiling. Croat. J. Med. 42:229–232, 2001.

    CAS  Google Scholar 

  137. Hawkins, T. L., Detter, J. C., and Richardson, P. M. Whole genome amplificationa —pplications and advances. Curr. Opin. Biotechnol. 13:65–67, 2002.

    Article  PubMed  CAS  Google Scholar 

  138. Telenius, H., Carter, N. P., Bebb, C. E., Nordenskjold, M., Ponder, B. A., and Tunnacliffe, A. Degenerate oligonucleotide-primed PCR: general amplification of target DAN by a single degenerate primer. Genomics 13:718–725, 1992.

    Article  PubMed  CAS  Google Scholar 

  139. Barbaux, S., Poirier, O., and Cambien, F. Use of degenerate oligonucleotide primed PCR (DOP-PCR) for the genotyping of low-concentration DNA samples. J. Mol. Med. 79:329–332, 2001.

    Article  PubMed  CAS  Google Scholar 

  140. Zhang, L., Cui X., Schmitt, K., Hubert, R., Navidi, W., and Arnheim, N. Whole genome amplification from a single cell: implications for genetic analysis. Proc. Natl. Acad. Sci. USA 89:5847–5851, 1992.

    Article  PubMed  CAS  Google Scholar 

  141. Dean, F. B., Hosono, S., Fang, L., et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99:5261–5266, 2002.

    Article  PubMed  CAS  Google Scholar 

  142. Cheung, V. G. and Nelson, S. F. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proc. Natl. Acad. Sci. USA 93:14,676–14,679, 1996.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Humana Press, a part of Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Cruz, T.D. (2006). Molecular Analysis for Forensic Casework and Parentage Testing. In: Coleman, W.B., Tsongalis, G.J. (eds) Molecular Diagnostics. Humana Press. https://doi.org/10.1385/1-59259-928-1:495

Download citation

  • DOI: https://doi.org/10.1385/1-59259-928-1:495

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-356-5

  • Online ISBN: 978-1-59259-928-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics