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Volumn 6, Issue 11S, 2009, Pages S13-

Computational methods for discovering structural variation with next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; DNA SEQUENCE; GENETIC VARIABILITY; GENOME; GENOMICS; HUMAN; METHODOLOGY; NUCLEOTIDE SEQUENCE; REVIEW;

EID: 70449704529     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.1374     Document Type: Article
Times cited : (437)

References (49)
  • 1
    • 4444291843 scopus 로고    scopus 로고
    • Detection of large-scale variation in the human genome
    • Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949-951 (2004).
    • (2004) Nat. Genet , vol.36 , pp. 949-951
    • Iafrate, A.J.1
  • 2
    • 22844451617 scopus 로고    scopus 로고
    • Fine-scale structural variation of the human genome
    • Tuzun, E. et al. Fine-scale structural variation of the human genome. Nat. Genet. 37, 727-732 (2005).
    • (2005) Nat. Genet , vol.37 , pp. 727-732
    • Tuzun, E.1
  • 3
    • 35348988679 scopus 로고    scopus 로고
    • Paired-end mapping reveals extensive structural variation in the human genome
    • One of the first studies to use NGS data to detect structural variants, including using the linking signature for detecting insertions larger than the insert size
    • Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426 (2007). One of the first studies to use NGS data to detect structural variants, including using the linking signature for detecting insertions larger than the insert size.
    • (2007) Science , vol.318 , pp. 420-426
    • Korbel, J.O.1
  • 4
    • 31144469134 scopus 로고    scopus 로고
    • Structural variation in the human genome
    • Feuk, L., Carson, A.R. & Scherer, S.W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85-97 (2006).
    • (2006) Nat. Rev. Genet , vol.7 , pp. 85-97
    • Feuk, L.1    Carson, A.R.2    Scherer, S.W.3
  • 5
    • 43049143055 scopus 로고    scopus 로고
    • Mapping and sequencing of structural variation from eight human genomes
    • Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64 (2008).
    • (2008) Nature , vol.453 , pp. 56-64
    • Kidd, J.M.1
  • 6
    • 52949141845 scopus 로고    scopus 로고
    • Integrated detection and population-genetic analysis of SNPs and copy number variation
    • McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166-1174 (2008).
    • (2008) Nat. Genet , vol.40 , pp. 1166-1174
    • McCarroll, S.A.1
  • 7
    • 52949093111 scopus 로고    scopus 로고
    • Systematic assessment of copy number variant detection via genome-wide SNP genotyping
    • Cooper, G.M., Zerr, T., Kidd, J.M., Eichler, E.E. & Nickerson, D.A. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat. Genet. 40, 1199-1203 (2008).
    • (2008) Nat. Genet , vol.40 , pp. 1199-1203
    • Cooper, G.M.1    Zerr, T.2    Kidd, J.M.3    Eichler, E.E.4    Nickerson, D.A.5
  • 8
    • 46249087524 scopus 로고    scopus 로고
    • A robust framework for detecting structural variations in a genome
    • Lee, S., Cheran, E. & Brudno, M. A robust framework for detecting structural variations in a genome. Bioinformatics 24, i59-i67 (2008).
    • (2008) Bioinformatics , vol.24 , pp. i59-i67
    • Lee, S.1    Cheran, E.2    Brudno, M.3
  • 9
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • The first high coverage NGS dataset of an individual. This data set has been used in many subsequent studies
    • Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008). The first high coverage NGS dataset of an individual. This data set has been used in many subsequent studies.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 10
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • One of the first comprehensive tools for structural variant detection; supports most basic signatures and uses soft clustering
    • Hormozdiari, F., Alkan, C., Eichler, E.E. & Sahinalp, S.C. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res. 19, 1270-1278 (2009). One of the first comprehensive tools for structural variant detection; supports most basic signatures and uses soft clustering.
    • (2009) Genome Res , vol.19 , pp. 1270-1278
    • Hormozdiari, F.1    Alkan, C.2    Eichler, E.E.3    Sahinalp, S.C.4
  • 11
    • 67649580757 scopus 로고    scopus 로고
    • MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions
    • Lee, S., Hormozdiari, F., Alkan, C. & Brudno, M. MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods 6, 473-474 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 473-474
    • Lee, S.1    Hormozdiari, F.2    Alkan, C.3    Brudno, M.4
  • 12
    • 84988045542 scopus 로고    scopus 로고
    • The first method to use a distribution-based clustering approach, allowing the detection of smaller indels, and explicitly modeling heterozygosity
    • The first method to use a distribution-based clustering approach, allowing the detection of smaller indels, and explicitly modeling heterozygosity.
  • 13
    • 34347353237 scopus 로고    scopus 로고
    • Copy-number variation and association studies of human disease
    • McCarroll, S.A. & Altshuler, D.M. Copy-number variation and association studies of human disease. Nat. Genet. 39, S37-S42 (2007).
    • (2007) Nat. Genet , vol.39 , pp. S37-S42
    • McCarroll, S.A.1    Altshuler, D.M.2
  • 14
    • 1542515338 scopus 로고    scopus 로고
    • A census of human cancer genes
    • Futreal, P.A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-183 (2004).
    • (2004) Nat. Rev. Cancer , vol.4 , pp. 177-183
    • Futreal, P.A.1
  • 15
    • 34347354302 scopus 로고    scopus 로고
    • Mutational and selective effects on copy-number variants in the human genome
    • Cooper, G.M., Nickerson, D.E. & Eichler, E.E. Mutational and selective effects on copy-number variants in the human genome. Nat. Genet. 39, S22-S29 (2007).
    • (2007) Nat. Genet , vol.39 , pp. S22-S29
    • Cooper, G.M.1    Nickerson, D.E.2    Eichler, E.E.3
  • 16
    • 0037934515 scopus 로고    scopus 로고
    • End-sequence profiling: Sequence-based analysis of aberrant genomes
    • Volik, S. et al. End-sequence profiling: Sequence-based analysis of aberrant genomes. Proc. Natl. Acad. Sci. USA 100, 7696-7701 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7696-7701
    • Volik, S.1
  • 17
  • 18
    • 34247481814 scopus 로고    scopus 로고
    • Strong association of de novo copy number mutations with autism
    • Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
    • (2007) Science , vol.316 , pp. 445-449
    • Sebat, J.1
  • 19
    • 0242300619 scopus 로고    scopus 로고
    • Alpha-synuclein locus triplication causes Parkinson’s disease
    • Singleton, A.B. et al. Alpha-synuclein locus triplication causes Parkinson’s disease. Science 302, 841 (2003).
    • (2003) Science , vol.302 , pp. 841
    • Singleton, A.B.1
  • 20
    • 57149099396 scopus 로고    scopus 로고
    • Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
    • Kim, P.M. et al. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 18, 1865-1874 (2008).
    • (2008) Genome Res , vol.18 , pp. 1865-1874
    • Kim, P.M.1
  • 21
    • 17344371740 scopus 로고    scopus 로고
    • High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
    • Pinkel, D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207-211 (1998).
    • (1998) Nat. Genet , vol.20 , pp. 207-211
    • Pinkel, D.1
  • 22
    • 3242808027 scopus 로고    scopus 로고
    • Large-scale copy number polymorphism in the human genome
    • Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525-528 (2004).
    • (2004) Science , vol.305 , pp. 525-528
    • Sebat, J.1
  • 23
    • 20544462642 scopus 로고    scopus 로고
    • Segmental duplications and copy-number variation in the human genome
    • Sharp, A.J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77, 78-88 (2005).
    • (2005) Am. J. Hum. Genet , vol.77 , pp. 78-88
    • Sharp, A.J.1
  • 24
    • 34347339520 scopus 로고    scopus 로고
    • Methods and strategies for analyzing copy number variation using DNA microarrays
    • Carter, N.P. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet. 39, S16-S21 (2007).
    • (2007) Nat. Genet , vol.39 , pp. S16-S21
    • Carter, N.P.1
  • 25
    • 34447577485 scopus 로고    scopus 로고
    • The International HapMap Project
    • International HapMap Consortium. The International HapMap Project. Nature 437, 1299-1320 (2005).
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 26
    • 29444441336 scopus 로고    scopus 로고
    • High-resolution survey of deletion polymorphism in the human genome
    • Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E. & Pritchard, J.K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75-81 (2006).
    • (2006) Nat. Genet , vol.38 , pp. 75-81
    • Conrad, D.F.1    Rews, T.D.2    Carter, N.P.3    Hurles, M.E.4    Pritchard, J.5
  • 27
    • 29444450702 scopus 로고    scopus 로고
    • Common deletions and SNPs are in linkage disequilibrium in the human genome
    • Hinds, D.A., Kloek, A.P., Jen, M., Chen, X. & Frazer, K.A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet. 38, 82-85 (2006).
    • (2006) Nat. Genet , vol.38 , pp. 82-85
    • Hinds, D.A.1    Kloek, A.P.2    Jen, M.3    Chen, X.4    Frazer, K.A.5
  • 28
    • 29444457877 scopus 로고    scopus 로고
    • Common deletion polymorphisms in the human genome
    • McCarroll, S.A. et al. Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86-92 (2006).
    • (2006) Nat. Genet , vol.38 , pp. 86-92
    • McCarroll, S.A.1
  • 29
    • 67650287133 scopus 로고    scopus 로고
    • Identification and frequency estimation of inversion polymorphisms from haplotype data
    • (ed. Batzoglou, S.) 418433 (Springer, Berlin
    • Sindi, S. & Raphael, B. Identification and frequency estimation of inversion polymorphisms from haplotype data. in Research in Computational Molecular Biology: Proc. RECOMB 2009 vol. 5541 (ed. Batzoglou, S.) 418433 (Springer, Berlin, 2009).
    • (2009) Research in Computational Molecular Biology: Proc. RECOMB 2009 Vol. 5541
    • Sindi, S.1    Raphael, B.2
  • 30
    • 37749025169 scopus 로고    scopus 로고
    • Primer: Sequencing-the next generation
    • Rusk, N. & Kiermer, V. Primer: Sequencing-the next generation. Nat. Methods 5, 15 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 15
    • Rusk, N.1    Kiermer, V.2
  • 31
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145 (2008).
    • (2008) Nat. Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 32
    • 67349209853 scopus 로고    scopus 로고
    • Next-generation sequencing techniques
    • Ansorge, W.J. Next-generation sequencing techniques. New Biotechnol. 25, 195-203 (2009).
    • (2009) New Biotechnol , vol.25 , pp. 195-203
    • Ansorge, W.J.1
  • 33
    • 46649099510 scopus 로고    scopus 로고
    • Genomes project
    • Siva, N. 1000 Genomes project. Nat. Biotechnol. 26, 256 (2008).
    • (2008) Nat. Biotechnol , vol.26 , pp. 256
    • Siva, N.1
  • 34
    • 42949123953 scopus 로고    scopus 로고
    • Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLOS Comput
    • Bashir, A., Volik, S., Collins, C., Bafna, V. & Raphael, B.J. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLOS Comput. Biol. 4, e1000051 (2008).
    • (2008) Biol , vol.4 , pp. e1000051
    • Bashir, A.1    Volik, S.2    Collins, C.3    Bafna, V.4    Raphael, B.J.5
  • 35
    • 44349191457 scopus 로고    scopus 로고
    • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
    • The first study to use the DOC signatures in NGS data, detecting CNVs in tumor samples
    • Campbell, P.J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722-729 (2008). The first study to use the DOC signatures in NGS data, detecting CNVs in tumor samples.
    • (2008) Nat. Genet , vol.40 , pp. 722-729
    • Campbell, P.J.1
  • 36
    • 33748271469 scopus 로고    scopus 로고
    • An initial map of insertion and deletion (INDEL) variation in the human genome
    • Mills, R.E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182-1190 (2006).
    • (2006) Genome Res , vol.16 , pp. 1182-1190
    • Mills, R.E.1
  • 38
    • 0037047628 scopus 로고    scopus 로고
    • Recent segmental duplications in the human genome
    • Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003-1007 (2002).
    • (2002) Science , vol.297 , pp. 1003-1007
    • Bailey, J.A.1
  • 39
    • 24344459066 scopus 로고    scopus 로고
    • A genome-wide comparison of recent chimpanzee and human segmental duplications
    • Cheng, Z. et al. A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature 437, 88-93 (2005).
    • (2005) Nature , vol.437 , pp. 88-93
    • Cheng, Z.1
  • 40
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm, J.C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105 (2008).
    • (2008) Nucleic Acids Res , vol.36 , pp. e105
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 41
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • Harismendy, O. et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10, R32 (2009).
    • (2009) Genome Biol , vol.10 , pp. R32
    • Harismendy, O.1
  • 42
    • 62549131646 scopus 로고    scopus 로고
    • PEMer: A computational framework with simulation- based error models for inferring genomic structural variants from massive paired-end sequencing data
    • Korbel, J.O. et al. PEMer: A computational framework with simulation- based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 10, R23 (2009).
    • (2009) Genome Biol , vol.10 , pp. R23
    • Korbel, J.O.1
  • 43
    • 69749090013 scopus 로고    scopus 로고
    • Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding
    • doi:10.1101/ gr.091868.109, 22 June
    • McKernan, K.J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527-1541; doi:10.1101/ gr.091868.109 (22 June 2009).
    • (2009) Genome Res , vol.19 , pp. 1527-1541
    • McKernan, K.J.1
  • 44
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high resolution mapping of genomic structural variation
    • doi:10.1038/ nmeth.1363 (9 August
    • Chen, K. et al. BreakDancer: An algorithm for high resolution mapping of genomic structural variation. Nat. Methods 6, 677-681; doi:10.1038/ nmeth.1363 (9 August 2009).
    • (2009) Nat. Methods , vol.6 , pp. 677-681
    • Chen, K.1
  • 45
    • 58149218240 scopus 로고    scopus 로고
    • High-resolution mapping of copy-number alterations with massively parallel sequencing
    • Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 99-103
    • Chiang, D.Y.1
  • 46
    • 58149234737 scopus 로고    scopus 로고
    • Real-time DNA sequencing from single polymerase molecules
    • Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
    • (2009) Science , vol.323 , pp. 133-138
    • Eid, J.1
  • 47
    • 33846006596 scopus 로고    scopus 로고
    • A comprehensive analysis of common copy-number variations in the human genome
    • Wong, K.K. et al. A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet. 80, 91-104 (2007).
    • (2007) Am. J. Hum. Genet , vol.80 , pp. 91-104
    • Wong, K.K.1
  • 48
    • 33751329250 scopus 로고    scopus 로고
    • Global variation in copy number in the human genome
    • Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444-454 (2006).
    • (2006) Nature , vol.444 , pp. 444-454
    • Redon, R.1
  • 49
    • 0642344260 scopus 로고    scopus 로고
    • Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster
    • Locke, D.P. et al. Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster. Genome Biol. 4, R50 (2003).
    • (2003) Genome Biol , vol.4 , pp. R50
    • Locke, D.P.1


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