메뉴 건너뛰기




Volumn 4, Issue 4, 2010, Pages 228-231

Shotgun metagenomics of biological stains using ultra-deep DNA sequencing

Author keywords

454 pyrosequencing; Biological stain; Forensic science; Species identification; Ultra deep DNA sequencing

Indexed keywords

BACTERIAL DNA; FUNGAL DNA; MICROSATELLITE DNA; MITOCHONDRIAL DNA; VIRUS DNA;

EID: 77957551861     PISSN: 18724973     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fsigen.2009.10.001     Document Type: Article
Times cited : (28)

References (34)
  • 1
    • 0027996118 scopus 로고
    • DNA typing in forensic science. I. Theory and background
    • H.C. Lee, C. Ladd, and M.T. Bourke DNA typing in forensic science. I. Theory and background Am. J. Forensic Med. Pathol. 15 1994 269 282
    • (1994) Am. J. Forensic Med. Pathol. , vol.15 , pp. 269-282
    • Lee, H.C.1    Ladd, C.2    Bourke, M.T.3
  • 2
    • 0036020080 scopus 로고    scopus 로고
    • Role of molecular diagnostics in forensic science
    • A. Linacre, and D. Graham Role of molecular diagnostics in forensic science Expert Rev. Mol. Diagn. 2 2002 346 353
    • (2002) Expert Rev. Mol. Diagn. , vol.2 , pp. 346-353
    • Linacre, A.1    Graham, D.2
  • 3
    • 0026345151 scopus 로고
    • Problems associated with the DNA analysis of stains
    • S. Rand, P. Wiegand, and B. Brinkmann Problems associated with the DNA analysis of stains Int. J. Legal Med. 104 1991 293 297
    • (1991) Int. J. Legal Med. , vol.104 , pp. 293-297
    • Rand, S.1    Wiegand, P.2    Brinkmann, B.3
  • 4
    • 34250315289 scopus 로고    scopus 로고
    • Simplified low-copy-number DNA analysis by post-PCR purification
    • P.J. Smith, and J. Ballantyne Simplified low-copy-number DNA analysis by post-PCR purification J. Forensic Sci. 52 2007 820 829
    • (2007) J. Forensic Sci. , vol.52 , pp. 820-829
    • Smith, P.J.1    Ballantyne, J.2
  • 5
    • 59849099685 scopus 로고    scopus 로고
    • The low-template-DNA (stochastic) threshold - Its determination relative to risk analysis for national DNA databases
    • P. Gill, R. Puch-Solis, and J. Curran The low-template-DNA (stochastic) threshold - its determination relative to risk analysis for national DNA databases Forensic Sci. Int. Genet. 3 2009 104 111
    • (2009) Forensic Sci. Int. Genet. , vol.3 , pp. 104-111
    • Gill, P.1    Puch-Solis, R.2    Curran, J.3
  • 6
    • 0027974076 scopus 로고
    • Sequential multiplex amplification (SMA) of genetic loci: A method for recovering template DNA for subsequent analyses of additional loci
    • M. Lorente, J.A. Lorente, and M.R. Wilson Sequential multiplex amplification (SMA) of genetic loci: a method for recovering template DNA for subsequent analyses of additional loci Int. J. Legal Med. 107 1994 156 158
    • (1994) Int. J. Legal Med. , vol.107 , pp. 156-158
    • Lorente, M.1    Lorente, J.A.2    Wilson, M.R.3
  • 7
    • 33847043874 scopus 로고    scopus 로고
    • A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA
    • C. Meissner, P. Bruse, and E. Mueller A new sensitive short pentaplex (ShoP) PCR for typing of degraded DNA Forensic Sci. Int. 166 2007 121 127
    • (2007) Forensic Sci. Int. , vol.166 , pp. 121-127
    • Meissner, C.1    Bruse, P.2    Mueller, E.3
  • 8
    • 33645844551 scopus 로고    scopus 로고
    • PCR microfluidic devices for DNA amplification
    • C. Zhang, J. Xu, and W. Ma PCR microfluidic devices for DNA amplification Biotechnol. Adv. 24 2006 243 284
    • (2006) Biotechnol. Adv. , vol.24 , pp. 243-284
    • Zhang, C.1    Xu, J.2    Ma, W.3
  • 9
    • 62649132171 scopus 로고    scopus 로고
    • Microfluidic DNA amplification - A review
    • Y. Zhang, and P. Ozdemir Microfluidic DNA amplification - a review Anal. Chim. Acta 638 2009 115 125
    • (2009) Anal. Chim. Acta , vol.638 , pp. 115-125
    • Zhang, Y.1    Ozdemir, P.2
  • 10
    • 33845569857 scopus 로고    scopus 로고
    • The utility of whole genome amplification for typing compromised forensic samples
    • A.L. Barber, and D.R. Foran The utility of whole genome amplification for typing compromised forensic samples J. Forensic Sci. 51 2006 1344 1349
    • (2006) J. Forensic Sci. , vol.51 , pp. 1344-1349
    • Barber, A.L.1    Foran, D.R.2
  • 11
    • 33846471929 scopus 로고    scopus 로고
    • Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples
    • K.N. Ballantyne, R.A. van Oorschot, and R.J. Mitchell Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples Forensic Sci. Int. 166 2007 35 41
    • (2007) Forensic Sci. Int. , vol.166 , pp. 35-41
    • Ballantyne, K.N.1    Van Oorschot, R.A.2    Mitchell, R.J.3
  • 12
    • 35348903113 scopus 로고    scopus 로고
    • Study of animal species (human, dog and cat) identification using a multiplex single-base primer extension reaction in the cytochrome b gene
    • S. Nakaki, D. Hino, and M. Miyoshi 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. 173 2007 97 102
    • (2007) Forensic Sci. Int. , vol.173 , pp. 97-102
    • Nakaki, S.1    Hino, D.2    Miyoshi, M.3
  • 13
    • 34548679130 scopus 로고    scopus 로고
    • Identification of mammal species using species-specific DNA pyrosequencing
    • A.O. Karlsson, and G. Holmlund Identification of mammal species using species-specific DNA pyrosequencing Forensic Sci. Int. 173 2007 16 20
    • (2007) Forensic Sci. Int. , vol.173 , pp. 16-20
    • Karlsson, A.O.1    Holmlund, G.2
  • 14
    • 38849140917 scopus 로고    scopus 로고
    • A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene
    • S.S. Tobe, and A.M. Linacre A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochrome b gene Electrophoresis 29 2008 340 347
    • (2008) Electrophoresis , vol.29 , pp. 340-347
    • Tobe, S.S.1    Linacre, A.M.2
  • 15
    • 44849107120 scopus 로고    scopus 로고
    • 454 life sciences: Illuminating the future of genome sequencing and personalized medicine
    • K. Patrick 454 life sciences: illuminating the future of genome sequencing and personalized medicine Yale J. Biol. Med. 80 2007 191 194
    • (2007) Yale J. Biol. Med. , vol.80 , pp. 191-194
    • Patrick, K.1
  • 16
    • 0036007337 scopus 로고    scopus 로고
    • TWGDAM validation of AmpFlSTR PCR amplification kits for forensic DNA casework
    • C.L. Holt, M. Buoncristiani, and J.M. Wallin TWGDAM validation of AmpFlSTR PCR amplification kits for forensic DNA casework J. Forensic Sci. 47 2002 66 96
    • (2002) J. Forensic Sci. , vol.47 , pp. 66-96
    • Holt, C.L.1    Buoncristiani, M.2    Wallin, J.M.3
  • 17
    • 21644484236 scopus 로고    scopus 로고
    • DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR
    • S. Kochl, H. Niederstatter, and W. Parson DNA extraction and quantitation of forensic samples using the phenol-chloroform method and real-time PCR Methods Mol. Biol. 297 2005 13 30
    • (2005) Methods Mol. Biol. , vol.297 , pp. 13-30
    • Kochl, S.1    Niederstatter, H.2    Parson, W.3
  • 18
    • 33750550654 scopus 로고    scopus 로고
    • Quantity versus quality: Optimal methods for cell-free DNA isolation from plasma of pregnant women
    • C.J. Jorgez, D.D. Dang, and J.L. Simpson Quantity versus quality: optimal methods for cell-free DNA isolation from plasma of pregnant women Genet. Med. 8 2006 615 619
    • (2006) Genet. Med. , vol.8 , pp. 615-619
    • Jorgez, C.J.1    Dang, D.D.2    Simpson, J.L.3
  • 19
    • 27644443339 scopus 로고    scopus 로고
    • Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA
    • E.K. Hanson, and J. Ballantyne Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA Anal. Biochem. 346 2005 246 257
    • (2005) Anal. Biochem. , vol.346 , pp. 246-257
    • Hanson, E.K.1    Ballantyne, J.2
  • 20
    • 39449089394 scopus 로고    scopus 로고
    • Parallel tagged sequencing on the 454 platform
    • M. Meyer, U. Stenzel, and M. Hofreiter Parallel tagged sequencing on the 454 platform Nat. Protoc. 3 2008 267 278
    • (2008) Nat. Protoc. , vol.3 , pp. 267-278
    • Meyer, M.1    Stenzel, U.2    Hofreiter, M.3
  • 21
  • 22
    • 43349107538 scopus 로고    scopus 로고
    • Using RepeatMasker to identify repetitive elements in genomic sequences
    • N. Chen Using RepeatMasker to identify repetitive elements in genomic sequences Curr. Protoc. Bioinformatics 2004 Chapter 4:Unit 4 10
    • (2004) Curr. Protoc. Bioinformatics
    • Chen, N.1
  • 23
    • 0000374167 scopus 로고    scopus 로고
    • Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples
    • W. Abu Al-Soud, and P. Radstrom Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples Appl. Environ. Microbiol. 64 1998 3748 3753
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3748-3753
    • Abu Al-Soud, W.1    Radstrom, P.2
  • 24
    • 46049099151 scopus 로고    scopus 로고
    • Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
    • S.L. Salzberg, D.D. Sommer, and M.C. Schatz Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A BMC Genomics 9 2008 204
    • (2008) BMC Genomics , vol.9 , pp. 204
    • Salzberg, S.L.1    Sommer, D.D.2    Schatz, M.C.3
  • 25
    • 0037203829 scopus 로고    scopus 로고
    • Genome sequence of the plant pathogen Ralstonia solanacearum
    • M. Salanoubat, S. Genin, and F. Artiguenave Genome sequence of the plant pathogen Ralstonia solanacearum Nature 415 2002 497 502
    • (2002) Nature , vol.415 , pp. 497-502
    • Salanoubat, M.1    Genin, S.2    Artiguenave, F.3
  • 26
    • 0023190848 scopus 로고
    • A physical map of the Escherichia coli K12 genome
    • C.L. Smith, J.G. Econome, and A. Schutt A physical map of the Escherichia coli K12 genome Science 236 1987 1448 1453
    • (1987) Science , vol.236 , pp. 1448-1453
    • Smith, C.L.1    Econome, J.G.2    Schutt, A.3
  • 27
    • 0027861139 scopus 로고
    • Mapping and sequencing the nuclear genome of the yeast Saccharomyces cerevisiae: Strategies and results of the European enterprise
    • B. Dujon Mapping and sequencing the nuclear genome of the yeast Saccharomyces cerevisiae: strategies and results of the European enterprise Cold Spring Harb. Symp. Quant. Biol. 58 1993 357 366
    • (1993) Cold Spring Harb. Symp. Quant. Biol. , vol.58 , pp. 357-366
    • Dujon, B.1
  • 28
    • 33745252555 scopus 로고    scopus 로고
    • Genomic analysis of host-pathogen interaction between Fusarium graminearum and wheat during early stages of disease development
    • R.S. Goswami, J.R. Xu, and F. Trail Genomic analysis of host-pathogen interaction between Fusarium graminearum and wheat during early stages of disease development Microbiology 152 2006 1877 1890
    • (2006) Microbiology , vol.152 , pp. 1877-1890
    • Goswami, R.S.1    Xu, J.R.2    Trail, F.3
  • 29
    • 29244442741 scopus 로고    scopus 로고
    • Genome sequencing and analysis of Aspergillus oryzae
    • M. Machida, K. Asai, and M. Sano Genome sequencing and analysis of Aspergillus oryzae Nature 438 2005 1157 1161
    • (2005) Nature , vol.438 , pp. 1157-1161
    • MacHida, M.1    Asai, K.2    Sano, M.3
  • 31
    • 44649090674 scopus 로고    scopus 로고
    • Gene prediction in metagenomic fragments: A large scale machine learning approach
    • K.J. Hoff, M. Tech, and T. Lingner Gene prediction in metagenomic fragments: a large scale machine learning approach BMC Bioinformatics 9 2008 217
    • (2008) BMC Bioinformatics , vol.9 , pp. 217
    • Hoff, K.J.1    Tech, M.2    Lingner, T.3
  • 32
    • 56749119854 scopus 로고    scopus 로고
    • Sequencing the nuclear genome of the extinct woolly mammoth
    • W. Miller, D.I. Drautz, and A. Ratan Sequencing the nuclear genome of the extinct woolly mammoth Nature 456 2008 387 390
    • (2008) Nature , vol.456 , pp. 387-390
    • Miller, W.1    Drautz, D.I.2    Ratan, A.3
  • 33
    • 33751073995 scopus 로고    scopus 로고
    • Sequencing and analysis of Neanderthal genomic DNA
    • J.P. Noonan, G. Coop, and S. Kudaravalli Sequencing and analysis of Neanderthal genomic DNA Science 314 2006 1113 1118
    • (2006) Science , vol.314 , pp. 1113-1118
    • Noonan, J.P.1    Coop, G.2    Kudaravalli, S.3
  • 34
    • 48049116437 scopus 로고    scopus 로고
    • A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures
    • S.S. Tobe, and A.M. Linacre A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures Forensic Sci. Int. Genet. 2 2008 249 256
    • (2008) Forensic Sci. Int. Genet. , vol.2 , pp. 249-256
    • Tobe, S.S.1    Linacre, A.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.