메뉴 건너뛰기




Volumn 13, Issue 3, 2012, Pages

An integrative probabilistic model for identification of structural variation in sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; DNA SEQUENCE; DNA STRUCTURE; INTERMETHOD COMPARISON; PROBABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL MODEL; STRUCTURAL VARIATION; CHROMOSOME INVERSION; CHROMOSOME MAP; GENE DELETION; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; NUCLEOTIDE REPEAT;

EID: 84858853457     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2012-13-3-r22     Document Type: Article
Times cited : (107)

References (52)
  • 6
    • 78650791604 scopus 로고    scopus 로고
    • Analysis of next-generation genomic data in cancer: accomplishments and challenges.
    • 10.1093/hmg/ddq391, 2953747, 20843826
    • Ding L, Wendl M, Koboldt D, Mardis E. Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet 2010, 19:R188. 10.1093/hmg/ddq391, 2953747, 20843826.
    • (2010) Hum Mol Genet , vol.19
    • Ding, L.1    Wendl, M.2    Koboldt, D.3    Mardis, E.4
  • 7
    • 80053542444 scopus 로고    scopus 로고
    • Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.
    • 3278838, 22373069
    • Wittler R, Chauve C. Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. BMC Bioinformatics 2011, 12:S21. 3278838, 22373069.
    • (2011) BMC Bioinformatics , vol.12
    • Wittler, R.1    Chauve, C.2
  • 8
    • 57049101718 scopus 로고    scopus 로고
    • Comparative genomics of wild type yeast strains unveils important genome diversity.
    • 10.1186/1471-2164-9-524, 2588607, 18983662
    • Carreto L, Eiriz M, Gomes A, Pereira P, Schuller D, Santos M. Comparative genomics of wild type yeast strains unveils important genome diversity. BMC Genomics 2008, 9:524. 10.1186/1471-2164-9-524, 2588607, 18983662.
    • (2008) BMC Genomics , vol.9 , pp. 524
    • Carreto, L.1    Eiriz, M.2    Gomes, A.3    Pereira, P.4    Schuller, D.5    Santos, M.6
  • 9
    • 77955275027 scopus 로고    scopus 로고
    • Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster.
    • 10.1093/gbe/evq001, 2839345, 20333226
    • Cridland J, Thornton K. Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster. Genome Biol Evol 2010, 2:83. 10.1093/gbe/evq001, 2839345, 20333226.
    • (2010) Genome Biol Evol , vol.2 , pp. 83
    • Cridland, J.1    Thornton, K.2
  • 11
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing.
    • 10.1038/nmeth.1374, 19844226
    • Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 2009, 6:S13-S20. 10.1038/nmeth.1374, 19844226.
    • (2009) Nat Methods , vol.6
    • Medvedev, P.1    Stanciu, M.2    Brudno, M.3
  • 12
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping.
    • 10.1038/nrg2958, 21358748
    • Alkan C, Coe B, Eichler E. Genome structural variation discovery and genotyping. Nat Rev Genet 2011, 12:363-376. 10.1038/nrg2958, 21358748.
    • (2011) Nat Rev Genet , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.2    Eichler, E.3
  • 13
    • 77950348516 scopus 로고    scopus 로고
    • Genome variation discovery with high-throughput sequencing data.
    • 10.1093/bib/bbp058, 20053733
    • Dalca A, Brudno M. Genome variation discovery with high-throughput sequencing data. Brief Bioinformatics 2010, 11:3. 10.1093/bib/bbp058, 20053733.
    • (2010) Brief Bioinformatics , vol.11 , pp. 3
    • Dalca, A.1    Brudno, M.2
  • 21
    • 77958508815 scopus 로고    scopus 로고
    • SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.
    • 10.1093/bioinformatics/btq528, 20876606
    • Abel H, Duncavage E, Becker N, Armstrong J, Magrini V, Pfeifer J. SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics 2010, 26:2684. 10.1093/bioinformatics/btq528, 20876606.
    • (2010) Bioinformatics , vol.26 , pp. 2684
    • Abel, H.1    Duncavage, E.2    Becker, N.3    Armstrong, J.4    Magrini, V.5    Pfeifer, J.6
  • 24
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly.
    • 10.1038/nmeth.1527, 3115693, 21102452
    • Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods 2011, 8:61-65. 10.1038/nmeth.1527, 3115693, 21102452.
    • (2011) Nat Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 25
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second-generation sequencing.
    • 10.1101/gr.101360.109, 2928494, 20508146
    • Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res 2010, 20:1165-1173. 10.1101/gr.101360.109, 2928494, 20508146.
    • (2010) Genome Res , vol.20 , pp. 1165-1173
    • Schatz, M.C.1    Delcher, A.L.2    Salzberg, S.L.3
  • 26
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage.
    • 10.1101/gr.092981.109, 2752127, 19657104
    • Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19:1586-1592. 10.1101/gr.092981.109, 2752127, 19657104.
    • (2009) Genome Res , vol.19 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 29
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing.
    • 10.1186/1471-2105-10-80, 2667514, 19267900
    • Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009, 10:80. 10.1186/1471-2105-10-80, 2667514, 19267900.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.T.2
  • 30
    • 79953855362 scopus 로고    scopus 로고
    • Accurate and exact CNV identification from targeted high-throughput sequence data.
    • 10.1186/1471-2164-12-184, 3088570, 21486468
    • Nord A, Lee M, King M, Walsh T. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics 2011, 12:184. 10.1186/1471-2164-12-184, 3088570, 21486468.
    • (2011) BMC Genomics , vol.12 , pp. 184
    • Nord, A.1    Lee, M.2    King, M.3    Walsh, T.4
  • 31
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
    • 10.1101/gr.114876.110, 3106330, 21324876
    • Abyzov A, Urban A, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011, 21:974. 10.1101/gr.114876.110, 3106330, 21324876.
    • (2011) Genome Res , vol.21 , pp. 974
    • Abyzov, A.1    Urban, A.2    Snyder, M.3    Gerstein, M.4
  • 33
    • 66349083341 scopus 로고    scopus 로고
    • A geometric approach for classification and comparison of structural variants.
    • 10.1093/bioinformatics/btp208, 2687962, 19477992
    • Sindi S, Helman E, Bashir A, Raphael BJ. A geometric approach for classification and comparison of structural variants. Bioinformatics 2009, 25:i222-230. 10.1093/bioinformatics/btp208, 2687962, 19477992.
    • (2009) Bioinformatics , vol.25
    • Sindi, S.1    Helman, E.2    Bashir, A.3    Raphael, B.J.4
  • 34
    • 77951860138 scopus 로고    scopus 로고
    • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.
    • 10.1101/gr.102970.109, 2860164, 20308636
    • Quinlan A, Clark R, Sokolova S, Leibowitz M, Zhang Y, Hurles M, Mell J, Hall I. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 2010, 20:623. 10.1101/gr.102970.109, 2860164, 20308636.
    • (2010) Genome Res , vol.20 , pp. 623
    • Quinlan, A.1    Clark, R.2    Sokolova, S.3    Leibowitz, M.4    Zhang, Y.5    Hurles, M.6    Mell, J.7    Hall, I.8
  • 35
    • 77954205450 scopus 로고    scopus 로고
    • Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
    • 10.1093/bioinformatics/btq216, 2881400, 20529927
    • Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, Alkan C, Eichler E, Sahinalp S. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 2010, 26:i350. 10.1093/bioinformatics/btq216, 2881400, 20529927.
    • (2010) Bioinformatics , vol.26
    • Hormozdiari, F.1    Hajirasouliha, I.2    Dao, P.3    Hach, F.4    Yorukoglu, D.5    Alkan, C.6    Eichler, E.7    Sahinalp, S.8
  • 36
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
    • 10.1093/bioinformatics/btp394, 2781750, 19561018
    • Ye K, Schulz M, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25:2865. 10.1093/bioinformatics/btp394, 2781750, 19561018.
    • (2009) Bioinformatics , vol.25 , pp. 2865
    • Ye, K.1    Schulz, M.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 37
    • 79959965448 scopus 로고    scopus 로고
    • InGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data.
    • 10.1093/nar/gkr506, 3125812, 21715388
    • Qi J, Zhao F. inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res 2011, 39:W567. 10.1093/nar/gkr506, 3125812, 21715388.
    • (2011) Nucleic Acids Res , vol.39
    • Qi, J.1    Zhao, F.2
  • 38
    • 78649309503 scopus 로고    scopus 로고
    • Detecting copy number variation with mated short reads.
    • 10.1101/gr.106344.110, 2963824, 20805290
    • Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Res 2010, 20:1613. 10.1101/gr.106344.110, 2963824, 20805290.
    • (2010) Genome Res , vol.20 , pp. 1613
    • Medvedev, P.1    Fiume, M.2    Dzamba, M.3    Smith, T.4    Brudno, M.5
  • 39
    • 42949123953 scopus 로고    scopus 로고
    • Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.
    • 10.1371/journal.pcbi.1000051, 2278375, 18404202
    • Bashir A, Volik S, Collins C, Bafna V, Raphael B. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 2008, 4:e1000051. 10.1371/journal.pcbi.1000051, 2278375, 18404202.
    • (2008) PLoS Comput Biol , vol.4
    • Bashir, A.1    Volik, S.2    Collins, C.3    Bafna, V.4    Raphael, B.5
  • 40
    • 67649834757 scopus 로고    scopus 로고
    • Characterization of six human disease-associated inversion polymorphisms.
    • 10.1093/hmg/ddp187, 2701327, 19383631
    • Antonacci F, Kidd J, Marques-Bonet T, Ventura M, Siswara P, Jiang Z, Eichler E. Characterization of six human disease-associated inversion polymorphisms. Hum Mol Genet 2009, 18:2555. 10.1093/hmg/ddp187, 2701327, 19383631.
    • (2009) Hum Mol Genet , vol.18 , pp. 2555
    • Antonacci, F.1    Kidd, J.2    Marques-Bonet, T.3    Ventura, M.4    Siswara, P.5    Jiang, Z.6    Eichler, E.7
  • 41
    • 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 2008, 24:59-67.
    • (2008) Bioinformatics , vol.24 , pp. 59-67
    • Lee, S.1    Cheran, E.2    Brudno, M.3
  • 42
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.
    • Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 2009,
    • (2009) Genome Res
    • Hormozdiari, F.1    Alkan, C.2    Eichler, E.E.3    Sahinalp, S.C.4
  • 45
    • 84864927741 scopus 로고    scopus 로고
    • VCF (Variant Calling Format) version 4.1.
    • VCF (Variant Calling Format) version 4.1. , http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
  • 46
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: a mathematical analysis.
    • 10.1016/0888-7543(88)90007-9, 3294162
    • Lander E, Waterman M. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988, 2:231-239. 10.1016/0888-7543(88)90007-9, 3294162.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.1    Waterman, M.2
  • 48
    • 84864920419 scopus 로고    scopus 로고
    • Novocraft: Novoalign.
    • Novocraft: Novoalign. , http://www.novocraft.com/main/index.php
  • 49
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools.
    • 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
    • (2009) Bioinformatics , vol.25 , pp. 2078
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 51
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation.
    • Metzker M. Sequencing technologies - the next generation. Nat Rev Genet 2009, 11:31-46.
    • (2009) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.1
  • 52
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform.
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.