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Volumn 13, Issue , 2014, Pages 20-29

Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

Author keywords

Heteroplasmy; MiSeq; mtDNA; Next generation sequencing; Nextera; NextGENe

Indexed keywords

MITOCHONDRIAL DNA;

EID: 84904976036     PISSN: 18724973     EISSN: 18780326     Source Type: Journal    
DOI: 10.1016/j.fsigen.2014.05.007     Document Type: Article
Times cited : (94)

References (47)
  • 1
    • 84892736165 scopus 로고    scopus 로고
    • Forensic mitochondrial DNA analysis: Current practice and future potential
    • T. Melton, C. Holland, and M. Holland Forensic mitochondrial DNA analysis: current practice and future potential Forensic Sci. Rev. 24 2012 101 122
    • (2012) Forensic Sci. Rev. , vol.24 , pp. 101-122
    • Melton, T.1    Holland, C.2    Holland, M.3
  • 2
    • 67650654645 scopus 로고    scopus 로고
    • The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases
    • R.S. Just, M.D. Leney, S.M. Barritt, C.W. Los, B.C. Smith, and T.D. Holland et al. The use of mitochondrial DNA single nucleotide polymorphisms to assist in the resolution of three challenging forensic cases J. Forensic Sci. 54 2009 887 891
    • (2009) J. Forensic Sci. , vol.54 , pp. 887-891
    • Just, R.S.1    Leney, M.D.2    Barritt, S.M.3    Los, C.W.4    Smith, B.C.5    Holland, T.D.6
  • 4
    • 0035116598 scopus 로고    scopus 로고
    • Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: A case report
    • A. Salas, M.V. Lareu, and A. Carracedo Heteroplasmy in mtDNA and the weight of evidence in forensic mtDNA analysis: a case report Int. J. Legal Med. 114 2001 186 190
    • (2001) Int. J. Legal Med. , vol.114 , pp. 186-190
    • Salas, A.1    Lareu, M.V.2    Carracedo, A.3
  • 5
    • 80051932240 scopus 로고    scopus 로고
    • Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy
    • M.M. Holland, M.R. McQuillan, and K.A. O'Hanlon Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy Croat. Med. J. 52 2011 299 313
    • (2011) Croat. Med. J. , vol.52 , pp. 299-313
    • Holland, M.M.1    McQuillan, M.R.2    O'Hanlon, K.A.3
  • 6
    • 84862182131 scopus 로고    scopus 로고
    • Next-generation sequencing technologies and applications for human genetic history and forensics
    • E.C. Berglund, A. Kiialainen, and A-C. Syvänen Next-generation sequencing technologies and applications for human genetic history and forensics Invest. Genet. 2 2011 23 37
    • (2011) Invest. Genet. , vol.2 , pp. 23-37
    • Berglund, E.C.1    Kiialainen, A.2    Syvänen, A.-C.3
  • 7
    • 78650762588 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    • S. Fisher, A. Barry, J. Abreu, B. Minie, J. Nolan, and T.M. Delorey et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries Genome Biol. 12 2011 R1
    • (2011) Genome Biol. , vol.12 , pp. 1
    • Fisher, S.1    Barry, A.2    Abreu, J.3    Minie, B.4    Nolan, J.5    Delorey, T.M.6
  • 8
    • 84855295457 scopus 로고    scopus 로고
    • Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
    • M. Kircher, S. Sawyer, and M. Meyer Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform Nucleic Acids Res. 40 2012 e3
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3
    • Kircher, M.1    Sawyer, S.2    Meyer, M.3
  • 9
    • 77953218382 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
    • N.J. Lennon, R.E. Lintner, S. Anderson, P. Alvarez, A. Barry, and W. Brockman et al. A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454 Genome Biol. 11 2010 R15
    • (2010) Genome Biol. , vol.11 , pp. 15
    • Lennon, N.J.1    Lintner, R.E.2    Anderson, S.3    Alvarez, P.4    Barry, A.5    Brockman, W.6
  • 11
    • 80051566879 scopus 로고    scopus 로고
    • High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform
    • S.L. Fordyce, M.C. Ávila-Acros, E. Rockenbauer, C. Børsting, R. Frank-Hansen, and F.T. Petersen et al. High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform Biotechniques 51 2011 127 133
    • (2011) Biotechniques , vol.51 , pp. 127-133
    • Fordyce, S.L.1    Ávila-Acros, M.C.2    Rockenbauer, E.3    Børsting, C.4    Frank-Hansen, R.5    Petersen, F.T.6
  • 12
    • 84863981120 scopus 로고    scopus 로고
    • Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    • J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, and N. Fierer et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ISME J. 6 2012 1621 1624
    • (2012) ISME J. , vol.6 , pp. 1621-1624
    • Caporaso, J.G.1    Lauber, C.L.2    Walters, W.A.3    Berg-Lyons, D.4    Huntley, J.5    Fierer, N.6
  • 13
    • 84865956894 scopus 로고    scopus 로고
    • Sequence error storms and the landscape of mutations in cancer
    • S. Kirsch, and C.A. Klein Sequence error storms and the landscape of mutations in cancer PNAS 109 2012 14289 14290
    • (2012) PNAS , vol.109 , pp. 14289-14290
    • Kirsch, S.1    Klein, C.A.2
  • 14
    • 84865979581 scopus 로고    scopus 로고
    • Detection of ultra-rare mutations by next-generation sequencing
    • M.W. Schmitt, S.R. Kennedy, J.J. Salk, E.J. Fox, J.B. Hiatt, and L.A. Loeb Detection of ultra-rare mutations by next-generation sequencing PNAS 109 2012 14508 14513
    • (2012) PNAS , vol.109 , pp. 14508-14513
    • Schmitt, M.W.1    Kennedy, S.R.2    Salk, J.J.3    Fox, E.J.4    Hiatt, J.B.5    Loeb, L.A.6
  • 15
    • 77957925524 scopus 로고    scopus 로고
    • Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing
    • M.V. Zaragoza, J. Fass, M. Diegoli, D. Lin, and E. Arbustini Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing PLoS ONE 5 2010 e12295
    • (2010) PLoS ONE , vol.5 , pp. 12295
    • Zaragoza, M.V.1    Fass, J.2    Diegoli, M.3    Lin, D.4    Arbustini, E.5
  • 16
    • 79959467651 scopus 로고    scopus 로고
    • Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
    • H. Goto, B. Dickins, E. Afgan, I.M. Paul, J. Taylor, and K.D. Makova et al. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study Genome Biol. 12 2011 R59
    • (2011) Genome Biol. , vol.12 , pp. 59
    • Goto, H.1    Dickins, B.2    Afgan, E.3    Paul, I.M.4    Taylor, J.5    Makova, K.D.6
  • 18
    • 77955562856 scopus 로고    scopus 로고
    • Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes
    • M. Li, A. Schönberg, M. Schaefer, R. Schroeder, I. Nasidze, and M. Stoneking Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes Am. J. Hum. Genet. 87 2010 237 249
    • (2010) Am. J. Hum. Genet. , vol.87 , pp. 237-249
    • Li, M.1    Schönberg, A.2    Schaefer, M.3    Schroeder, R.4    Nasidze, I.5    Stoneking, M.6
  • 19
    • 84878116632 scopus 로고    scopus 로고
    • Transition to next generation analysis of the whole mitochondrial genome: A summary of molecular defects
    • S. Tang, J. Wang, V.W. Zhang, F-Y. Li, M. Landsverk, and H. Cui et al. Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects Hum. Mutat. 34 2013 882 893
    • (2013) Hum. Mutat. , vol.34 , pp. 882-893
    • Tang, S.1    Wang, J.2    Zhang, V.W.3    Li, F.-Y.4    Landsverk, M.5    Cui, H.6
  • 20
    • 84880874709 scopus 로고    scopus 로고
    • Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)
    • W. Parson, C. Strobl, G. Huber, B. Zimmermann, S.M. Gomes, and L. Souto et al. Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM) Forensic Sci. Int. Genet. 7 2013 543 549
    • (2013) Forensic Sci. Int. Genet. , vol.7 , pp. 543-549
    • Parson, W.1    Strobl, C.2    Huber, G.3    Zimmermann, B.4    Gomes, S.M.5    Souto, L.6
  • 22
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • M.A. Quail, M. Smith, P. Coupland, T.D. Otto, S.R. Harris, and T.R. Connor et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers BMC Genomics 13 2012 341 353
    • (2012) BMC Genomics , vol.13 , pp. 341-353
    • Quail, M.A.1    Smith, M.2    Coupland, P.3    Otto, T.D.4    Harris, S.R.5    Connor, T.R.6
  • 24
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • E.S. Lander, and M.S. Waterman Genomic mapping by fingerprinting random clones: a mathematical analysis Genomics 2 1988 231 239
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 25
    • 0037270487 scopus 로고    scopus 로고
    • DNA from buccal swabs recruited by mail: Evaluation of storage effects on long-term stability and suitability for multiplex polymerase chain reaction genotyping
    • B. Freeman, N. Smith, C. Curtis, L. Huckett, J. Mill, and I.W. Craig DNA from buccal swabs recruited by mail: evaluation of storage effects on long-term stability and suitability for multiplex polymerase chain reaction genotyping Behav. Genet. 33 2003 67 72
    • (2003) Behav. Genet. , vol.33 , pp. 67-72
    • Freeman, B.1    Smith, N.2    Curtis, C.3    Huckett, L.4    Mill, J.5    Craig, I.W.6
  • 26
    • 64849084181 scopus 로고    scopus 로고
    • Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences
    • L. Fendt, B. Zimmermann, M. Daniaux, and W. Parson Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences BMC Genomics 10 2009 139 149
    • (2009) BMC Genomics , vol.10 , pp. 139-149
    • Fendt, L.1    Zimmermann, B.2    Daniaux, M.3    Parson, W.4
  • 27
    • 0029986876 scopus 로고    scopus 로고
    • Automated sequencing of mitochondrial DNA
    • M. Tanaka, M. Hayakawa, and T. Ozawa Automated sequencing of mitochondrial DNA Methods Enzymol. 264 1996 407 421
    • (1996) Methods Enzymol. , vol.264 , pp. 407-421
    • Tanaka, M.1    Hayakawa, M.2    Ozawa, T.3
  • 28
    • 84904962224 scopus 로고    scopus 로고
    • Illumina Inc. (Part #15027987 Rev. B.)
    • Illumina Inc. Nextera® DNA Sample Preparation Guide 2012 (Part #15027987 Rev. B.) http://supportres.illumina.com/documents/myillumina/2a3297c5- 8a34-4fc5-a148-3e16666fd65e/nextera-dna-sample-prep-guide-15027987-b.pdf
    • (2012) Nextera® DNA Sample Preparation Guide
  • 31
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 32
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • T.F. Smith, and M.S. Waterman Identification of common molecular subsequences J. Mol. Biol. 147 1981 195 197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 33
    • 84908219488 scopus 로고
    • Statistical methods for assessing agreement between two methods of clinical measurement
    • J.M. Bland, and D.G. Altman Statistical methods for assessing agreement between two methods of clinical measurement Lancet 1 1986 307 310
    • (1986) Lancet , vol.1 , pp. 307-310
    • Bland, J.M.1    Altman, D.G.2
  • 34
    • 0032884749 scopus 로고    scopus 로고
    • Measuring agreement in method comparison studies
    • J.M. Bland, and D.G. Altman Measuring agreement in method comparison studies Stat Methods Med. Res. 8 1999 135 160
    • (1999) Stat Methods Med. Res. , vol.8 , pp. 135-160
    • Bland, J.M.1    Altman, D.G.2
  • 35
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • O. Harismendy, P.C. Ng, R.L. Strausberg, X. Wang, T.B. Stockwell, and K.Y. Beeson et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies Genome Biol. 10 2009 R32
    • (2009) Genome Biol. , vol.10 , pp. 32
    • Harismendy, O.1    Ng, P.C.2    Strausberg, R.L.3    Wang, X.4    Stockwell, T.B.5    Beeson, K.Y.6
  • 36
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • J.C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Nucleic Acids Res. 36 2008 e105
    • (2008) Nucleic Acids Res. , vol.36 , pp. 105
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 39
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
    • A.E. Minoche, J.C. Dohm, and H. Himmelbauer Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems Genome Biol. 12 2011 R112
    • (2011) Genome Biol. , vol.12 , pp. 112
    • Minoche, A.E.1    Dohm, J.C.2    Himmelbauer, H.3
  • 40
    • 67650074197 scopus 로고    scopus 로고
    • Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
    • W. Qu, S-I. Hashimoto, and S. Morishita Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing Genome Res. 19 2009 1309 1315
    • (2009) Genome Res. , vol.19 , pp. 1309-1315
    • Qu, W.1    Hashimoto, S.-I.2    Morishita, S.3
  • 42
    • 67349134670 scopus 로고    scopus 로고
    • Investigation of heteroplasmy in the human mitochondrial DNA control region: A synthesis of observations from more than 5000 global population samples
    • J.A. Irwin, J.L. Saunier, H. Niederstätter, K.M. Strouss, K.A. Sturk, and T.M. Diegoli et al. Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples J. Mol. Evol. 68 2009 516 527
    • (2009) J. Mol. Evol. , vol.68 , pp. 516-527
    • Irwin, J.A.1    Saunier, J.L.2    Niederstätter, H.3    Strouss, K.M.4    Sturk, K.A.5    Diegoli, T.M.6
  • 44
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • K. Tamura, and M. Nei Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees Mol. Biol. Evol. 10 1993 512 526
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 45
    • 0026046333 scopus 로고
    • African populations and the evolution of human mitochondrial DNA
    • L. Vigilant, M. Stoneking, H. Harpending, K. Hawkes, and A.C. Wilson African populations and the evolution of human mitochondrial DNA Science 253 1991 1503 1507
    • (1991) Science , vol.253 , pp. 1503-1507
    • Vigilant, L.1    Stoneking, M.2    Harpending, H.3    Hawkes, K.4    Wilson, A.C.5
  • 46
    • 0027496790 scopus 로고
    • Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
    • J. Wakeley Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA J. Mol. Evol. 37 1993 613 623
    • (1993) J. Mol. Evol. , vol.37 , pp. 613-623
    • Wakeley, J.1
  • 47
    • 0029997198 scopus 로고    scopus 로고
    • Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II
    • I.I. Pavel, M.J. Wadhams, R.K. Roby, M.M. Holland, V.W. Weedn, and T.J. Parsons Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II Nat. Genet. 12 1996 417 420
    • (1996) Nat. Genet. , vol.12 , pp. 417-420
    • Pavel, I.I.1    Wadhams, M.J.2    Roby, R.K.3    Holland, M.M.4    Weedn, V.W.5    Parsons, T.J.6


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