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Volumn 17, Issue 1, 2016, Pages

The next generation of target capture technologies - large DNA fragment enrichment and sequencing determines regional genomic variation of high complexity

Author keywords

DNA sequencing; DNA target capture; Genomic resequencing; MHC haplotype; Targeted enrichment

Indexed keywords

NUCLEOTIDE; OLIGONUCLEOTIDE; PRIMER DNA;

EID: 84991800774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2836-6     Document Type: Article
Times cited : (55)

References (46)
  • 2
    • 84893720512 scopus 로고    scopus 로고
    • Enrichment of target sequences for next-generation sequencing applications in research and diagnostics
    • Altmuller J, Budde BS, Nurnberg P. Enrichment of target sequences for next-generation sequencing applications in research and diagnostics. Biol Chem. 2014;395(2):231-7.
    • (2014) Biol Chem , vol.395 , Issue.2 , pp. 231-237
    • Altmuller, J.1    Budde, B.S.2    Nurnberg, P.3
  • 4
    • 84959376910 scopus 로고    scopus 로고
    • Advances in Clinical Next-Generation Sequencing: Target Enrichment and Sequencing Technologies
    • Ballester LY, Luthra R, Kanagal-Shamanna R, Singh RR. Advances in Clinical Next-Generation Sequencing: Target Enrichment and Sequencing Technologies. Expert Rev Mol Diagn. 2016;16(3):357-72.
    • (2016) Expert Rev Mol Diagn , vol.16 , Issue.3 , pp. 357-372
    • Ballester, L.Y.1    Luthra, R.2    Kanagal-Shamanna, R.3    Singh, R.R.4
  • 5
    • 84862777457 scopus 로고    scopus 로고
    • Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities
    • Lin X, Tang W, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res. 2012;288(1-2):67-76.
    • (2012) Hear Res , vol.288 , Issue.1-2 , pp. 67-76
    • Lin, X.1    Tang, W.2    Ahmad, S.3    Lu, J.4    Colby, C.C.5    Zhu, J.6    Yu, Q.7
  • 7
    • 84868616287 scopus 로고    scopus 로고
    • Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder
    • Steinberg KM, Ramachandran D, Patel VC, Shetty AC, Cutler DJ, Zwick ME. Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder. Mol Autism. 2012;3(1):8.
    • (2012) Mol Autism , vol.3 , Issue.1 , pp. 8
    • Steinberg, K.M.1    Ramachandran, D.2    Patel, V.C.3    Shetty, A.C.4    Cutler, D.J.5    Zwick, M.E.6
  • 8
    • 84856879501 scopus 로고    scopus 로고
    • Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies
    • Ghosh S, Krux F, Binder V, Gombert M, Niehues T, Feyen O, Laws HJ, Borkhardt A. Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies. Scand J Immunol. 2012;75(3):350-4.
    • (2012) Scand J Immunol , vol.75 , Issue.3 , pp. 350-354
    • Ghosh, S.1    Krux, F.2    Binder, V.3    Gombert, M.4    Niehues, T.5    Feyen, O.6    Laws, H.J.7    Borkhardt, A.8
  • 9
    • 84862776732 scopus 로고    scopus 로고
    • Targeted genomic sequencing identifies PRRT2 mutations as a cause of paroxysmal kinesigenic choreoathetosis
    • Li J, Zhu X, Wang X, Sun W, Feng B, Du T, Sun B, Niu F, Wei H, Wu X, et al. Targeted genomic sequencing identifies PRRT2 mutations as a cause of paroxysmal kinesigenic choreoathetosis. J Med Genet. 2012;49(2):76-8.
    • (2012) J Med Genet , vol.49 , Issue.2 , pp. 76-78
    • Li, J.1    Zhu, X.2    Wang, X.3    Sun, W.4    Feng, B.5    Du, T.6    Sun, B.7    Niu, F.8    Wei, H.9    Wu, X.10
  • 15
    • 84880807131 scopus 로고    scopus 로고
    • An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing
    • Cao H, Wu J, Wang Y, Jiang H, Zhang T, Liu X, Xu Y, Liang D, Gao P, Sun Y, et al. An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing. PLoS One. 2013;8(7):e69388.
    • (2013) PLoS One , vol.8 , Issue.7
    • Cao, H.1    Wu, J.2    Wang, Y.3    Jiang, H.4    Zhang, T.5    Liu, X.6    Xu, Y.7    Liang, D.8    Gao, P.9    Sun, Y.10
  • 18
    • 79955724657 scopus 로고    scopus 로고
    • Comparing de novo genome assembly: the long and short of it
    • Narzisi G, Mishra B. Comparing de novo genome assembly: the long and short of it. PLoS One. 2011;6(4):e19175.
    • (2011) PLoS One , vol.6 , Issue.4
    • Narzisi, G.1    Mishra, B.2
  • 19
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: computational challenges and solutions
    • Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2011;13(1):36-46.
    • (2011) Nat Rev Genet , vol.13 , Issue.1 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 20
    • 77955463346 scopus 로고    scopus 로고
    • Third generation DNA sequencing: pacific biosciences' single molecule real time technology
    • McCarthy A. Third generation DNA sequencing: pacific biosciences' single molecule real time technology. Chem Biol. 2010;17(7):675-6.
    • (2010) Chem Biol , vol.17 , Issue.7 , pp. 675-676
    • McCarthy, A.1
  • 21
    • 84907952658 scopus 로고    scopus 로고
    • A first look at the Oxford Nanopore MinION sequencer
    • Mikheyev AS, Tin MM. A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour. 2014;14(6):1097-102.
    • (2014) Mol Ecol Resour , vol.14 , Issue.6 , pp. 1097-1102
    • Mikheyev, A.S.1    Tin, M.M.2
  • 24
    • 84975741816 scopus 로고    scopus 로고
    • Characterization of structural variants with single molecule and hybrid sequencing approaches
    • Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics. 2014;30(24):3458-66.
    • (2014) Bioinformatics , vol.30 , Issue.24 , pp. 3458-3466
    • Ritz, A.1    Bashir, A.2    Sindi, S.3    Hsu, D.4    Hajirasouliha, I.5    Raphael, B.J.6
  • 27
    • 84866654229 scopus 로고    scopus 로고
    • New prediction model for probe specificity in an allele-specific extension reaction for haplotype-specific extraction (HSE) of Y chromosome mixtures
    • Rothe J, Watkins Jr NE, Nagy M. New prediction model for probe specificity in an allele-specific extension reaction for haplotype-specific extraction (HSE) of Y chromosome mixtures. PLoS One. 2012;7(9):e45955.
    • (2012) PLoS One , vol.7 , Issue.9
    • Rothe, J.1    Watkins, N.E.2    Nagy, M.3
  • 29
    • 84946405803 scopus 로고    scopus 로고
    • The dichotomy between disease phenotype databases and the implications for understanding complex diseases involving the major histocompatibility complex
    • Clark PM, Kunkel M, Monos DS. The dichotomy between disease phenotype databases and the implications for understanding complex diseases involving the major histocompatibility complex. Int J Immunogenet. 2015;42(6):413-22.
    • (2015) Int J Immunogenet , vol.42 , Issue.6 , pp. 413-422
    • Clark, P.M.1    Kunkel, M.2    Monos, D.S.3
  • 30
    • 84867128206 scopus 로고    scopus 로고
    • Interrogating the major histocompatibility complex with high-throughput genomics
    • de Bakker PI, Raychaudhuri S. Interrogating the major histocompatibility complex with high-throughput genomics. Hum Mol Genet. 2012;21(R1):R29-36.
    • (2012) Hum Mol Genet , vol.21 , Issue.R1 , pp. R29-R36
    • de Bakker, P.I.1    Raychaudhuri, S.2
  • 32
    • 79954423741 scopus 로고    scopus 로고
    • The MHC, disease and selection
    • Trowsdale J. The MHC, disease and selection. Immunol Lett. 2011;137(1-2):1-8.
    • (2011) Immunol Lett , vol.137 , Issue.1-2 , pp. 1-8
    • Trowsdale, J.1
  • 37
    • 84934769334 scopus 로고    scopus 로고
    • Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
    • Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 2015;43(6):e37.
    • (2015) Nucleic Acids Res , vol.43 , Issue.6
    • Schirmer, M.1    Ijaz, U.Z.2    D'Amore, R.3    Hall, N.4    Sloan, W.T.5    Quince, C.6
  • 38
    • 84939794352 scopus 로고    scopus 로고
    • Towards allele-level human leucocyte antigens genotyping-assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq
    • Duke JL, Lind C, Mackiewicz K, Ferriola D, Papazoglou A, Derbeneva O, Wallace D, Monos DS. Towards allele-level human leucocyte antigens genotyping-assessing two next-generation sequencing platforms: Ion Torrent Personal Genome Machine and Illumina MiSeq. Int J Immunogenet. 2015;42(5):346-58.
    • (2015) Int J Immunogenet , vol.42 , Issue.5 , pp. 346-358
    • Duke, J.L.1    Lind, C.2    Mackiewicz, K.3    Ferriola, D.4    Papazoglou, A.5    Derbeneva, O.6    Wallace, D.7    Monos, D.S.8
  • 41
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. 2002;12(4):656-64.
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 42
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: software for nucleic acid folding and hybridization
    • Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008;453:3-31.
    • (2008) Methods Mol Biol , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 43
    • 77957340554 scopus 로고    scopus 로고
    • Microtubule actin crosslinking factor 1 regulates the Balbiani body and animal-vegetal polarity of the zebrafish oocyte
    • Gupta T, Marlow FL, Ferriola D, Mackiewicz K, Dapprich J, Monos D, Mullins MC. Microtubule actin crosslinking factor 1 regulates the Balbiani body and animal-vegetal polarity of the zebrafish oocyte. PLoS Genet. 2010;6(8):e1001073.
    • (2010) PLoS Genet , vol.6 , Issue.8
    • Gupta, T.1    Marlow, F.L.2    Ferriola, D.3    Mackiewicz, K.4    Dapprich, J.5    Monos, D.6    Mullins, M.C.7
  • 44
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.