Forensic Science International: Genetics
Volume 3, Issue 2 , Pages 96-103 , March 2009

A new multiplex-PCR comprising autosomal and y-specific STRs and mitochondrial DNA to analyze highly degraded material

  • Nicole von Wurmb-Schwark

      Affiliations

    • Department of Legal Medicine, Christian-Albrechts-University of Kiel, Germany
    • Corresponding Author InformationCorresponding author. Department of Legal Medicine, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel, Germany. Tel.: +49 431 597 3633; fax: +49 431 597 3612.
  • ,
  • Andrea Preusse-Prange

      Affiliations

    • Department of Legal Medicine, Christian-Albrechts-University of Kiel, Germany
  • ,
  • Anke Heinrich

      Affiliations

    • Department of Legal Medicine, Christian-Albrechts-University of Kiel, Germany
  • ,
  • Eva Simeoni

      Affiliations

    • Department of Legal Medicine, Christian-Albrechts-University of Kiel, Germany
  • ,
  • Thomas Bosch

      Affiliations

    • Zoological Institute, Chrinstian-Albrechts-University of Kiel, Germany
  • ,
  • Thorsten Schwark

      Affiliations

    • Department of Legal Medicine, Christian-Albrechts-University of Kiel, Germany

Received 18 March 2008 ,Revised 15 October 2008 ,Accepted 14 November 2008.

References 

  1. Asamura H, Fujimori S, Ota M, Fukushima H. MiniSTR multiplex systems based on non-CODIS loci for analysis of degraded DNA samples. Forensic Sci. Int. 2007;173:7–15
  2. Grubwieser P, Mühlmann R, Berger B, Niederstätter H, Pavlic M, Parson W. A new “miniSTR-multiplex” displaying reduced amplicon lengths for the analysis of degraded DNA. Int. J. Legal Med. 2006;120:115–120
  3. Pääbo S, Higuchi RG, Wilson AC. Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology. J. Biol. Chem. 1989;264:9709–9712
  4. Bramanti A, Hummel S, Schultes T, Hermann B. STR Allelic Frequencies in a German Skeleton Collection. Anthropol. Anz. 2000;58:45–49
  5. Butler JM, Ruitberg CM, Vallone PM. Capillary electrophoresis as a tool for optimization of multiplex PCR reactions. Fresen. J. Anal. Chem. 2001;369:200–205
  6. Yeung SHI, Greenspoon SA, McGuckian A, Crouse CA, Emrich CA, Ban J, et al. Rapid and high-throughput forensic short tandem repeat typing using a 96-lane microfabricated capillary array electrophoresis microdevice. J. Forensic Sci. 2006;51:740–747
  7. Holland MM, Cave CA, Holland CA, Bille TW. Development of a Quality, High Throughput DNA Analysis Procedure for Skeletal Samples to Assist with the Identification of Victims from the World Trade Center Attacks. Croat. Med. J. 2003;44:264–272
  8. Sajantila A, Ström M, Budowle B, Karhunen PJ, Peltonen L. The polymerase chain reaction and post-mortem forensic identity testing: application of amplified D1S80 and HLA-DQ alpha loci to the identification of fire victims. Forensic Sci. Int. 1991;51:23–34
  9. Copeland AR. Suicidal fire deaths revisited. Z. Rechtsmed. 1985;95:51–57
  10. Bohnert M, Rothschild MA. Complex suicides by self-incineration. Forensic Sci. Int. 2003;131:197–201
  11. Hoff-Olsen P, Mevag B, Staalstrom E, Hovde B, Egeland T, Olaisen B. Extraction of DNA from decomposed human tissue. An evaluation of five extraction methods for short tandem repeat typing. Forensic Sci. Int. 1999;105:171–183
  12. Deng Y-J, Li Y-Z, Yu X-G, Li L, Wu D-Y, Zhou J, et al. Preliminary DNA Identification for the Tsunami Victims in Thailand. Genomics Proteomics Bioinform. 2005;3:143–157
  13. Budimlija ZM, Lechpammer M, Popiolek D, Fogt F, Prinz M, Bieber FR. Forensic applications of laser capture microdissection: use in DNA-based parentage testing and platform validation. Croat. Med. J. 2005;46:549–555
  14. Turrina S, Atzei R, Filippini G, De Leo D. STR typing of archival Bouin's fluid-fixed paraffin-embedded tissue using new sensitive redesigned primers for three STR loci (CSF1P0, D8S1179 and D13S317). J. Forensic Legal Med. 2008;15:27–31
  15. Pfeiffer H, Hühne J, Ortmann C, Waterkamp K. Mitochondrial DNA typing from human axillary, pubic and head hair shafts—success rates and sequence comparisons. Int. J. Legal Med. 1999;112:287–290
  16. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–715
  17. Moreira D. Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acids Res. 1998;26:3309–3310
  18. Sutlovic D, Gojanovic MD, Andelinovic S, Gugic D, Primorac D. Taq polymerase reverses inhibition of quantitative real time polymerase chain reaction by humic acid. Croat. Med. J. 2005;46:556–562
  19. Poinar HN, Höss M, Bada JL, Päabo S. Amino acid racemization and the preservation of ancient DNA. Science. 1996;272:864–868
  20. Poinar HN, Stankiewicz BA. Protein preservation and DNA retrieval from ancient tissues. Proc. Natl. Acad. Sci. U.S.A. 1999;8426–8431
  21. von Wurmb-Schwark N, Schwark T, Harbeck M, Oehmichen M. A simple Duplex-PCR to evaluate the DNA quality of anthropological and forensic samples prior short tandem repeats typing. Legal Med. 2004;6:80–88
  22. Butler JM, Shen Y, McCord BR. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci. 2003;48:1054–1064
  23. Wiegand P, Klein R, Braunschweiger G, Hohoff C, Brinkmann B. Short amplicon STR multiplex for stain typing. Int. J. Legal Med. 2006;120:160–164
  24. Meissner C, Bruse P, Mueller E, Oehmichen M. A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA. Forensic Sci. Int. 2007;166:121–127
  25. Budowle B, Adams DE, Comey CC, Merrill CR. Mitochondrial DNA—a possible genetic material suitable for forensic analysis. In:  Lee HC,  Gaensslen RE editor. Advances in Forensic Science. Chicago, Illinois: Year Book Medical Publisher; 1990;p. 76–97
  26. Holland MM, Fisher DL, Mitchell LG, Rodriquez WC, Canik JJ, Merril CR, et al. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J. Forensic Sci. 1993;38:542–553
  27. Kontanis EJ, Reed FA. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J. Forensic Sci. 2006;51:795–804
  28. Nicklas JA, Buel E. Simultaneous determination of total human and male DNA using a Duplex real-time PCR assay. J. Forensic Sci. 2006;51:1005–1015
  29. Swango KL, Hudlow WR, Timken MD, Buoncristiani MR. Developmental validation of a multiplex qPCR assay for assessing the quantity and quality of nuclear DNA in forensic samples. Forensic Sci. Int. 2007;170:35–45
  30. Park MJ, Lee HY, Chung U, Kang SC, Shin KJ. Y-STR analysis of degraded DNA using reduced-size amplicons. Int. J. Legal Med. 2007;121:152–157
  31. Butler JM, Schoske R, Vallone PM, Kline MC, Redd AJ, Hammer MF. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci. Int. 2002;129:10–24
  32. Pfeiffer H, Forster P, Ortmann C, Brinkmann B. The results of an mtDNA study of 1200 inhabitants of a German village in comparison to other Caucasian databases an its relevance for forensic casework. Int. J. Legal Med. 2001;114:169–172
  33. Köchl S, Niederstätter H, Parson W. DNA extraction and quantitation of forensic samples using the phenol–chloroform method and real-time PCR. Methods Mol. Biol. 2005;297:13–30
  34. Fisher DA, Bode HR. Nucleotide sequence of an actin-encoding gene from Hydra attenuata: structural characteristics and evolutionary implications. Gene. 1989;84:55–64
  35. Butler JM. Short tandem repeat typing technologies used in human identity testing. BioTechniques. Suppl. Hum. Heritage Identity. 2007;43:S2–S5
  36. Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, Graziosi G, et al Evaluation of Y-chromosomal STRs: a multicenter study. Int. J. Legal Med. 1997;110:125–133
  37. von Wurmb-Schwark N, Bosinski H, Ritz-Timme S. What do the X and Y chromosomes tell us about sex and gender in forensic case analysis?. J. Forensic Legal Med. 2007;14:27–30
  38. Brinkmann B. Is the amelogenin sex test valid?. Int. J. Legal Med. 2002;116:63
  39. Schmidt D, Hummel S, Herrmann B. Multiplex X/Y-PCR improves sex identification in aDNA analysis. Am. J. Phys. Anthropol. 2003;121:337–341
  40. Vanderheyden N, Mai A, Gilissen A, Cassiman JJ, Decorte R. Identification and sequence analysis of discordant phenotypes between AmpFlSTR SGM Plus and PowerPlex 16. Int. J. Legal Med. 2007;121:297–301
  41. Junge A, Lederer T, Braunschweiger G, Madea B. Validation of the multiplex kit genRESMPX-2 for forensic casework analysis. Int. J. Legal Med. 2003;117:317–325
  42. Prinz M, Boll K, Baum H, Shaler B. Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci. Int. 1997;85:209–218
  43. Bourke MT, Scherczinger CA, Ladd C, Lee HC. NaOH Treatment to neutralize inhibitors of Taq polymerase. J. Forensic Sci. 1999;44:1046–1050
  44. Pfeiffer H, Brinkmann B, Hühne J, Rolf B, Morris AA, Steighner R, et al. Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography. Int. J. Legal Med. 1999;112:291–298

PII: S1872-4973(08)00178-6

doi: 10.1016/j.fsigen.2008.11.007

Forensic Science International: Genetics
Volume 3, Issue 2 , Pages 96-103 , March 2009