Forensic Science International: Genetics
Volume 4, Issue 4 , Pages 228-231 , July 2010

Shotgun metagenomics of biological stains using ultra-deep DNA sequencing

  • B. Brenig

      Affiliations

    • Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
    • Corresponding Author InformationCorresponding author. Tel.: +49 551 393383; fax: +49 551 393392.
    • ,
  • J. Beck

      Affiliations

    • Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
    • Chronix Biomedical GmbH, Goetheallee 8, 37073 Göttingen, Germany
    • ,
  • E. Schütz

      Affiliations

    • Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
    • Chronix Biomedical GmbH, Goetheallee 8, 37073 Göttingen, Germany

Received 28 November 2008 ,Revised 30 September 2009 ,Accepted 2 October 2009.

References 

  1. Lee HC, Ladd C, Bourke MT, et al. DNA typing in forensic science. I. Theory and background. Am. J. Forensic Med. Pathol. 1994;15:269–282
  2. Linacre A, Graham D. Role of molecular diagnostics in forensic science. Expert Rev. Mol. Diagn. 2002;2:346–353
  3. Rand S, Wiegand P, Brinkmann B. Problems associated with the DNA analysis of stains. Int. J. Legal Med. 1991;104:293–297
  4. Smith PJ, Ballantyne J. Simplified low-copy-number DNA analysis by post-PCR purification. J. Forensic Sci. 2007;52:820–829
  5. Gill P, Puch-Solis R, Curran J. The low-template-DNA (stochastic) threshold—its determination relative to risk analysis for national DNA databases. Forensic Sci. Int. Genet. 2009;3:104–111
  6. Lorente M, Lorente JA, Wilson MR, et al. Sequential multiplex amplification (SMA) of genetic loci: a method for recovering template DNA for subsequent analyses of additional loci. Int. J. Legal Med. 1994;107:156–158
  7. Meissner C, Bruse P, Mueller E, et al. A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA. Forensic Sci. Int. 2007;166:121–127
  8. Zhang C, Xu J, Ma W, et al. PCR microfluidic devices for DNA amplification. Biotechnol. Adv. 2006;24:243–284
  9. Zhang Y, Ozdemir P. Microfluidic DNA amplification—a review. Anal. Chim. Acta. 2009;638:115–125
  10. Barber AL, Foran DR. The utility of whole genome amplification for typing compromised forensic samples. J. Forensic Sci. 2006;51:1344–1349
  11. Ballantyne KN, van Oorschot RA, Mitchell RJ. Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples. Forensic Sci. Int. 2007;166:35–41
  12. Nakaki S, Hino D, Miyoshi M, et al. Study of animal species (human, dog and cat) identification using a multiplex single-base primer extension reaction in the cytochrome b gene. Forensic Sci. Int. 2007;173:97–102
  13. Karlsson AO, Holmlund G. Identification of mammal species using species-specific DNA pyrosequencing. Forensic Sci. Int. 2007;173:16–20
  14. Tobe SS, Linacre AM. A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene. Electrophoresis. 2008;29:340–347
  15. Patrick K. 454 life sciences: illuminating the future of genome sequencing and personalized medicine. Yale J. Biol. Med. 2007;80:191–194
  16. Holt CL, Buoncristiani M, Wallin JM, et al. TWGDAM validation of AmpFlSTR PCR amplification kits for forensic DNA casework. J. Forensic Sci. 2002;47:66–96
  17. Kochl S, Niederstatter 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
  18. Jorgez CJ, Dang DD, Simpson JL, et al. Quantity versus quality: optimal methods for cell-free DNA isolation from plasma of pregnant women. Genet. Med. 2006;8:615–619
  19. Hanson EK, Ballantyne J. Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA. Anal. Biochem. 2005;346:246–257
  20. Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat. Protoc. 2008;3:267–278
  21. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410
  22. Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics. 2004;Chapter 4:Unit 4 10
  23. Abu Al-Soud W, Radstrom P. Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 1998;64:3748–3753
  24. Salzberg SL, Sommer DD, Schatz MC, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics. 2008;9:204
  25. Salanoubat M, Genin S, Artiguenave F, et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature. 2002;415:497–502
  26. Smith CL, Econome JG, Schutt A, et al. A physical map of the Escherichia coli K12 genome. Science. 1987;236:1448–1453
  27. Dujon B. Mapping and sequencing the nuclear genome of the yeast Saccharomyces cerevisiae: strategies and results of the European enterprise. Cold Spring Harb. Symp. Quant. Biol. 1993;58:357–366
  28. Goswami RS, Xu JR, Trail F, et al. Genomic analysis of host–pathogen interaction between Fusarium graminearum and wheat during early stages of disease development. Microbiology. 2006;152:1877–1890
  29. Machida M, Asai K, Sano M, et al. Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005;438:1157–1161
  30. Foerstner KU, von Mering C, Bork P. Comparative analysis of environmental sequences: potential and challenges. Philos. Trans. R. Soc. Lond. B: Biol. Sci. 2006;361:519–523
  31. Hoff KJ, Tech M, Lingner T, et al. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics. 2008;9:217
  32. Miller W, Drautz DI, Ratan A, et al. Sequencing the nuclear genome of the extinct woolly mammoth. Nature. 2008;456:387–390
  33. Noonan JP, Coop G, Kudaravalli S, et al. Sequencing and analysis of Neanderthal genomic DNA. Science. 2006;314:1113–1118
  34. Tobe SS, Linacre AM. A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures. Forensic Sci. Int. Genet. 2008;2:249–256

PII: S1872-4973(09)00150-1

doi: 10.1016/j.fsigen.2009.10.001

Forensic Science International: Genetics
Volume 4, Issue 4 , Pages 228-231 , July 2010

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