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Volumn 370, Issue 1660, 2015, Pages

Partial uracil – DNA – glycosylase treatment for screening of ancient DNA

Author keywords

Ancient DNA; Authenticity; Barcodes; Flexibility; Library preparation; Target capture

Indexed keywords

ADAPTATION; GENETIC ANALYSIS; HYBRIDIZATION; LABORATORY METHOD; TYPE SPECIMEN;

EID: 84916210143     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2013.0624     Document Type: Article
Times cited : (326)

References (42)
  • 1
    • 0000832946 scopus 로고
    • Ancient DNA: Extraction, characterization, molecular cloning, and enzymatic amplification
    • Paabo S. 1989 Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939- 1943. (doi:10.1073/pnas.86.6.1939)
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 1939-1943
    • Paabo, S.1
  • 2
    • 84892911863 scopus 로고    scopus 로고
    • A paleogenomic perspective on evolution and gene function: New insights from ancient DNA
    • Shapiro B, Hofreiter M. 2014 A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343, 1236573. (doi:10.1126/science.1236573)
    • (2014) Science , vol.343 , pp. 1236573
    • Shapiro, B.1    Hofreiter, M.2
  • 4
    • 84890612289 scopus 로고    scopus 로고
    • Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment
    • Enk J, Rouillard JM, Poinar H. 2013 Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment. Biotechniques 55, 300-309.
    • (2013) Biotechniques , vol.55 , pp. 300-309
    • Enk, J.1    Rouillard, J.M.2    Poinar, H.3
  • 5
    • 84856281777 scopus 로고    scopus 로고
    • Case study: Enrichment of ancient mitochondrial DNA by hybridization capture
    • Horn S. 2012 Case study: enrichment of ancient mitochondrial DNA by hybridization capture. Methods Mol. Biol. 840, 189-195. (doi:10.1007/ 978-1-61779-516-9_22)
    • (2012) Methods Mol. Biol. , vol.840 , pp. 189-195
    • Horn, S.1
  • 6
    • 78649512174 scopus 로고    scopus 로고
    • Multiplexed DNA sequence capture of mitochondrial genomes using PCR products
    • Maricic T, Whitten M, Paabo S. 2010 Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5, e14004. (doi:10. 1371/journal.pone.0014004)
    • (2010) PLoS ONE , vol.5
    • Maricic, T.1    Whitten, M.2    Paabo, S.3
  • 7
    • 80053137140 scopus 로고    scopus 로고
    • Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the black death
    • Schuenemann VJ et al. 2011 Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the black death. Proc. Natl Acad. Sci. USA 108, E746-E752. (doi:10.1073/ pnas.1105107108)
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. E746-E752
    • Schuenemann, V.J.1
  • 8
    • 34848827224 scopus 로고    scopus 로고
    • Patterns of damage in genomic DNA sequences from a Neandertal
    • Briggs AW et al. 2007 Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14 616-14 621. (doi:10. 1073/pnas.0704665104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 14 616-14 621
    • Briggs, A.W.1
  • 9
    • 0035581087 scopus 로고    scopus 로고
    • DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
    • Hofreiter M et al. 2001 DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29, 4793-4799. (doi:10.1093/nar/29. 23.4793)
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4793-4799
    • Hofreiter, M.1
  • 10
    • 34848866065 scopus 로고    scopus 로고
    • Novel highresolution characterization of ancient DNA reveals C. U-type base modification events as the sole cause of post mortem miscoding lesions
    • Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A. 2007 Novel highresolution characterization of ancient DNA reveals C. U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 35, 5717-5728. (doi:10.1093/nar/gkm588)
    • (2007) Nucleic Acids Res. , vol.35 , pp. 5717-5728
    • Brotherton, P.1    Endicott, P.2    Sanchez, J.J.3    Beaumont, M.4    Barnett, R.5    Austin, J.6    Cooper, A.7
  • 11
    • 33748783644 scopus 로고    scopus 로고
    • Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA
    • Stiller M et al. 2006 Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc. Natl Acad. Sci. USA 103, 13 578-13 584. (doi:10.1073/pnas.0605327103)
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 13 578-13 584
    • Stiller, M.1
  • 12
    • 84876151646 scopus 로고    scopus 로고
    • A revised timescale for human evolution based on ancient mitochondrial genomes
    • Fu Q et al. 2013 A revised timescale for human evolution based on ancient mitochondrial genomes. Curr. Biol. 23, 553-559. (doi:10.1016/j.cub.2013. 02.044)
    • (2013) Curr. Biol. , vol.23 , pp. 553-559
    • Fu, Q.1
  • 13
    • 77950862213 scopus 로고    scopus 로고
    • Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
    • Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Paabo S. 2010 Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87. (doi:10.1093/nar/ gkp1163)
    • (2010) Nucleic Acids Res. , vol.38
    • Briggs, A.W.1    Stenzel, U.2    Meyer, M.3    Krause, J.4    Kircher, M.5    Paabo, S.6
  • 14
    • 84892367625 scopus 로고    scopus 로고
    • Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    • Raghavan M et al. 2014 Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87-91. (doi:10.1038/ nature12736)
    • (2014) Nature , vol.505 , pp. 87-91
    • Raghavan, M.1
  • 15
    • 84893961036 scopus 로고    scopus 로고
    • The genome of a Late Pleistocene human from a Clovis burial site in western Montana
    • Rasmussen M et al. 2014 The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225-229. (doi:10. 1038/nature13025)
    • (2014) Nature , vol.506 , pp. 225-229
    • Rasmussen, M.1
  • 17
    • 84892572735 scopus 로고    scopus 로고
    • A mitochondrial genome sequence of a hominin from Sima de los Huesos
    • Meyer M et al. 2014 A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403-406. (doi:10.1038/ nature12788)
    • (2014) Nature , vol.505 , pp. 403-406
    • Meyer, M.1
  • 18
    • 84890151805 scopus 로고    scopus 로고
    • Pulling out the 1%: Whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries
    • Carpenter ML et al. 2013 Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am. J. Hum. Genet. 93, 852-864. (doi:10.1016/j.ajhg.2013. 10.002)
    • (2013) Am. J. Hum. Genet. , vol.93 , pp. 852-864
    • Carpenter, M.L.1
  • 20
    • 59849113821 scopus 로고    scopus 로고
    • Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    • Gnirke A et al. 2009 Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182-189. (doi:10.1038/nbt.1523)
    • (2009) Nat. Biotechnol. , vol.27 , pp. 182-189
    • Gnirke, A.1
  • 21
    • 36549021060 scopus 로고    scopus 로고
    • Genome-wide in situ exon capture for selective resequencing
    • Hodges E et al. 2007 Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 1522-1527. (doi:10.1038/ng.2007.42)
    • (2007) Nat. Genet. , vol.39 , pp. 1522-1527
    • Hodges, E.1
  • 22
    • 84899568858 scopus 로고    scopus 로고
    • Ancient whole genome enrichment using baits built from modern DNA
    • Enk JM et al. 2014 Ancient whole genome enrichment using baits built from modern DNA. Mol. Biol. Evol. 31, 1292-1294. (doi:10.1093/ molbev/msu074)
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 1292-1294
    • Enk, J.M.1
  • 23
    • 78650762588 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    • Fisher S et al. 2011 A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1. (doi:10.1186/gb-2011-12-1-r1)
    • (2011) Genome Biol. , vol.12
    • Fisher, S.1
  • 24
    • 84860595791 scopus 로고    scopus 로고
    • Cost-effective, highthroughput DNA sequencing libraries for multiplexed target capture
    • Rohland N, Reich D. 2012 Cost-effective, highthroughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939-946. (doi:10.1101/gr.128124.111)
    • (2012) Genome Res. , vol.22 , pp. 939-946
    • Rohland, N.1    Reich, D.2
  • 25
    • 0034682945 scopus 로고    scopus 로고
    • Ancient DNA: Do it right or not at all
    • Cooper A, Poinar HN. 2000 Ancient DNA: do it right or not at all. Science 289, 1139. (doi:10.1126/ science.289.5482.1139b)
    • (2000) Science , vol.289 , pp. 1139
    • Cooper, A.1    Poinar, H.N.2
  • 26
    • 84855480116 scopus 로고    scopus 로고
    • Setting the stage: Building and working in an ancient DNA laboratory
    • Knapp M, Clarke AC, Horsburgh KA, Matisoo-Smith EA. 2012 Setting the stage: building and working in an ancient DNA laboratory. Ann. Anat. 194, 3-6. (doi:10.1016/j.aanat.2011.03.008)
    • (2012) Ann. Anat. , vol.194 , pp. 3-6
    • Knapp, M.1    Clarke, A.C.2    Horsburgh, K.A.3    Matisoo-Smith, E.A.4
  • 27
    • 61449219318 scopus 로고    scopus 로고
    • The Samara valley project: Late Bronze Age economy and ritual in the Russian steppes
    • Anthony DW et al. 2005 The Samara valley project: late Bronze Age economy and ritual in the Russian steppes. Eurasia Antiqua 11, 395-417.
    • (2005) Eurasia Antiqua , vol.11 , pp. 395-417
    • Anthony, D.W.1
  • 28
    • 84884624229 scopus 로고    scopus 로고
    • Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
    • Dabney J et al. 2013 Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15 758-15 763. (doi:10. 1073/pnas.1314445110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 15 758-15 763
    • Dabney, J.1
  • 29
    • 77956285690 scopus 로고    scopus 로고
    • Illumina sequencing library preparation for highly multiplexed target capture and sequencing
    • pdb prot5448
    • Meyer M, Kircher M. 2010 Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb prot5448. (doi:10.1101/pdb.prot5448)
    • (2010) Cold Spring Harb. Protoc. , vol.2010
    • Meyer, M.1    Kircher, M.2
  • 30
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • Kircher M, Sawyer S, Meyer M. 2012 Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3. (doi:10.1093/nar/gkr771)
    • (2012) Nucleic Acids Res. , vol.40
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 31
    • 84916196608 scopus 로고    scopus 로고
    • See
    • John JS. 2011 See https://github.com/jstjohn/ SeqPrep.
    • (2011)
    • John, J.S.1
  • 32
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760. (doi:10.1093/ bioinformatics/btp324)
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 33
    • 84859486099 scopus 로고    scopus 로고
    • A 'Copernican' reassessment of the human mitochondrial DNA tree from its root
    • Behar DM et al. 2012 A 'Copernican' reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675-684. (doi:10.1016/j. ajhg.2012.03.002)
    • (2012) Am. J. Hum. Genet. , vol.90 , pp. 675-684
    • Behar, D.M.1
  • 34
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842. (doi:10.1093/bio informatics/btq033)
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 35
    • 84879910635 scopus 로고    scopus 로고
    • MAPDAMAGE2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters
    • Jonsson H, Ginolhac A, Schubert M, Johnson PLF, Orlando L. 2013 MAPDAMAGE2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682-1684. (doi:10. 1093/bioinformatics/btt193)
    • (2013) Bioinformatics , vol.29 , pp. 1682-1684
    • Jonsson, H.1    Ginolhac, A.2    Schubert, M.3    Johnson, P.L.F.4    Orlando, L.5
  • 36
    • 53249132629 scopus 로고    scopus 로고
    • Identification of genetic variants using bar-coded multiplexed sequencing
    • Craig DW et al. 2008 Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5, 887-893. (doi:10.1038/ nmeth.1251)
    • (2008) Nat. Methods , vol.5 , pp. 887-893
    • Craig, D.W.1
  • 37
    • 69549139892 scopus 로고    scopus 로고
    • Direct multiplex sequencing (DMPS): A novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
    • Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. 2009 Direct multiplex sequencing (DMPS): a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res. 19, 1843-1848. (doi:10.1101/gr.095760.109)
    • (2009) Genome Res. , vol.19 , pp. 1843-1848
    • Stiller, M.1    Knapp, M.2    Stenzel, U.3    Hofreiter, M.4    Meyer, M.5
  • 38
    • 84867331947 scopus 로고    scopus 로고
    • A high-coverage genome sequence from an archaic Denisovan individual
    • Meyer M et al. 2012 A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222-226. (doi:10.1126/science. 1224344)
    • (2012) Science , vol.338 , pp. 222-226
    • Meyer, M.1
  • 39
    • 0025732374 scopus 로고
    • Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase
    • Varshney U, van de Sande JH. 1991 Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase. Biochemistry 30, 4055-4061. (doi:10.1021/bi00 230a033)
    • (1991) Biochemistry , vol.30 , pp. 4055-4061
    • Varshney, U.1    van de Sande, J.H.2
  • 40
    • 84857271408 scopus 로고    scopus 로고
    • Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
    • Dabney J, Meyer M. 2012 Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52, 87-94. (doi:10.2144/ 000113809)
    • (2012) Biotechniques , vol.52 , pp. 87-94
    • Dabney, J.1    Meyer, M.2
  • 41
    • 84859112401 scopus 로고    scopus 로고
    • Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
    • Sawyer S, Krause J, Guschanski K, Savolainen V. 2012 Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7, e34131. (doi:10.1371/journal. pone.0034131)
    • (2012) PLoS ONE , vol.7
    • Sawyer, S.1    Krause, J.2    Guschanski, K.3    Savolainen, V.4
  • 42
    • 84868087346 scopus 로고    scopus 로고
    • The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils
    • Allentoft ME et al. 2012 The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B 279, 4724-4733. (doi:10.1098/rspb. 2012.1745)
    • (2012) Proc. R. Soc. B , vol.279 , pp. 4724-4733
    • Allentoft, M.E.1


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