메뉴 건너뛰기




Volumn 8, Issue 5, 2013, Pages

PeSV-Fisher: Identification of Somatic and Non-Somatic Structural Variants Using Next Generation Sequencing Data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; BLOOD SAMPLING; CHROMOSOME INVERSION; CHROMOSOME TRANSLOCATION; CHRONIC LYMPHATIC LEUKEMIA; COMPUTER PROGRAM; GENE DELETION; GENETIC ANALYSIS; GENETIC PROCEDURES; GENETIC VARIABILITY; HUMAN; NEXT GENERATION SEQUENCING; PREDICTION; RELIABILITY; SEQUENCE ANALYSIS; SOMATIC MUTATION;

EID: 84877983704     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063377     Document Type: Article
Times cited : (16)

References (45)
  • 1
  • 3
    • 77950461601 scopus 로고    scopus 로고
    • Origins and functional impact of copy number variation in the human genome
    • Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
    • (2010) Nature , vol.464 , pp. 704-712
    • Conrad, D.F.1    Pinto, D.2    Redon, R.3    Feuk, L.4    Gokcumen, O.5
  • 4
    • 77949831756 scopus 로고    scopus 로고
    • Structural variation in the human genome and its role in disease
    • Stankiewicz P, Lupski JR, (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61: 437-455.
    • (2010) Annu Rev Med , vol.61 , pp. 437-455
    • Stankiewicz, P.1    Lupski, J.R.2
  • 5
    • 84975804424 scopus 로고    scopus 로고
    • Mapping copy number variation by population-scale genome sequencing
    • Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature 470: 59-65.
    • (2011) Nature , vol.470 , pp. 59-65
    • Mills, R.E.1    Walter, K.2    Stewart, C.3    Handsaker, R.E.4    Chen, K.5
  • 7
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing
    • Medvedev P, Stanciu M, Brudno M, (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6: S13-20.
    • (2009) Nat Methods , vol.6
    • Medvedev, P.1    Stanciu, M.2    Brudno, M.3
  • 8
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan C, Coe BP, Eichler EE, (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12: 363-376.
    • (2011) Nat Rev Genet , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 9
    • 35348988679 scopus 로고    scopus 로고
    • Paired-end mapping reveals extensive structural variation in the human genome
    • Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426.
    • (2007) Science , vol.318 , pp. 420-426
    • Korbel, J.O.1    Urban, A.E.2    Affourtit, J.P.3    Godwin, B.4    Grubert, F.5
  • 10
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
    • Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6: 677-681.
    • (2009) Nat Methods , vol.6 , pp. 677-681
    • Chen, K.1    Wallis, J.W.2    McLellan, M.D.3    Larson, D.E.4    Kalicki, J.M.5
  • 11
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC, (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 19: 1270-1278.
    • (2009) Genome Res , vol.19 , pp. 1270-1278
    • Hormozdiari, F.1    Alkan, C.2    Eichler, E.E.3    Sahinalp, S.C.4
  • 12
    • 43049143055 scopus 로고    scopus 로고
    • Mapping and sequencing of structural variation from eight human genomes
    • Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
    • (2008) Nature , vol.453 , pp. 56-64
    • Kidd, J.M.1    Cooper, G.M.2    Donahue, W.F.3    Hayden, H.S.4    Sampas, N.5
  • 13
    • 70349556543 scopus 로고    scopus 로고
    • Personalized copy number and segmental duplication maps using next-generation sequencing
    • Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41: 1061-1067.
    • (2009) Nat Genet , vol.41 , pp. 1061-1067
    • Alkan, C.1    Kidd, J.M.2    Marques-Bonet, T.3    Aksay, G.4    Antonacci, F.5
  • 14
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • Abyzov A, Urban AE, Snyder M, Gerstein M, (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21: 974-984.
    • (2011) Genome Res , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 15
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon S, Xuan Z, Makarov V, Ye K, Sebat J, (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19: 1586-1592.
    • (2009) Genome Res , vol.19 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 16
    • 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
    • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z, (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865-2871.
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 17
    • 79961007031 scopus 로고    scopus 로고
    • CREST maps somatic structural variation in cancer genomes with base-pair resolution
    • Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, et al. (2011) CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8: 652-654.
    • (2011) Nat Methods , vol.8 , pp. 652-654
    • Wang, J.1    Mullighan, C.G.2    Easton, J.3    Roberts, S.4    Heatley, S.L.5
  • 18
    • 77952814990 scopus 로고    scopus 로고
    • Detection and characterization of novel sequence insertions using paired-end next-generation sequencing
    • Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, et al. (2010) Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. Bioinformatics 26: 1277-1283.
    • (2010) Bioinformatics , vol.26 , pp. 1277-1283
    • Hajirasouliha, I.1    Hormozdiari, F.2    Alkan, C.3    Kidd, J.M.4    Birol, I.5
  • 19
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.
    • (2010) Genome Res , vol.20 , pp. 265-272
    • Li, R.1    Zhu, H.2    Ruan, J.3    Qian, W.4    Fang, X.5
  • 20
    • 78049412267 scopus 로고    scopus 로고
    • Diversity of human copy number variation and multicopy genes
    • Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, et al. (2010) Diversity of human copy number variation and multicopy genes. Science 330: 641-646.
    • (2010) Science , vol.330 , pp. 641-646
    • Sudmant, P.H.1    Kitzman, J.O.2    Antonacci, F.3    Alkan, C.4    Malig, M.5
  • 21
    • 78650663859 scopus 로고    scopus 로고
    • Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly
    • Wong K, Keane TM, Stalker J, Adams DJ, (2010) Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly. Genome Biol 11: R128.
    • (2010) Genome Biol , vol.11
    • Wong, K.1    Keane, T.M.2    Stalker, J.3    Adams, D.J.4
  • 22
    • 79959965448 scopus 로고    scopus 로고
    • inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data
    • Qi J, Zhao F, (2011) inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res 39: W567-575.
    • (2011) Nucleic Acids Res , vol.39
    • Qi, J.1    Zhao, F.2
  • 23
    • 78649309503 scopus 로고    scopus 로고
    • Detecting copy number variation with mated short reads
    • Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M, (2010) Detecting copy number variation with mated short reads. Genome Res 20: 1613-1622.
    • (2010) Genome Res , vol.20 , pp. 1613-1622
    • Medvedev, P.1    Fiume, M.2    Dzamba, M.3    Smith, T.4    Brudno, M.5
  • 24
    • 84858853457 scopus 로고    scopus 로고
    • An integrative probabilistic model for identification of structural variation in sequencing data
    • Sindi SS, Onal S, Peng L, Wu HT, Raphael BJ, (2012) An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol 13: R22.
    • (2012) Genome Biol , vol.13
    • Sindi, S.S.1    Onal, S.2    Peng, L.3    Wu, H.T.4    Raphael, B.J.5
  • 25
    • 77951860138 scopus 로고    scopus 로고
    • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, et al. (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res 20: 623-635.
    • (2010) Genome Res , vol.20 , pp. 623-635
    • Quinlan, A.R.1    Clark, R.A.2    Sokolova, S.3    Leibowitz, M.L.4    Zhang, Y.5
  • 26
    • 77954205450 scopus 로고    scopus 로고
    • Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
    • Hormozdiari F, Hajirasouliha I, Dao P, Hach F, Yorukoglu D, et al. (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26: i350-357.
    • (2010) Bioinformatics , vol.26
    • Hormozdiari, F.1    Hajirasouliha, I.2    Dao, P.3    Hach, F.4    Yorukoglu, D.5
  • 27
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: structural variant discovery by integrated paired-end and split-read analysis
    • Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333-i339.
    • (2012) Bioinformatics , vol.28
    • Rausch, T.1    Zichner, T.2    Schlattl, A.3    Stutz, A.M.4    Benes, V.5
  • 28
    • 78650959663 scopus 로고    scopus 로고
    • Massive genomic rearrangement acquired in a single catastrophic event during cancer development
    • Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, et al. (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144: 27-40.
    • (2011) Cell , vol.144 , pp. 27-40
    • Stephens, P.J.1    Greenman, C.D.2    Fu, B.3    Yang, F.4    Bignell, G.R.5
  • 29
    • 80054698731 scopus 로고    scopus 로고
    • Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
    • Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, et al. (2011) Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol 12: R103.
    • (2011) Genome Biol , vol.12
    • Kloosterman, W.P.1    Hoogstraat, M.2    Paling, O.3    Tavakoli-Yaraki, M.4    Renkens, I.5
  • 30
    • 80052916562 scopus 로고    scopus 로고
    • Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements
    • Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, et al. (2011) Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146: 889-903.
    • (2011) Cell , vol.146 , pp. 889-903
    • Liu, P.1    Erez, A.2    Nagamani, S.C.3    Dhar, S.U.4    Kolodziejska, K.E.5
  • 31
    • 79955416773 scopus 로고    scopus 로고
    • Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline
    • Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, et al. (2011) Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 20: 1916-1924.
    • (2011) Hum Mol Genet , vol.20 , pp. 1916-1924
    • Kloosterman, W.P.1    Guryev, V.2    van Roosmalen, M.3    Duran, K.J.4    de Bruijn, E.5
  • 32
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 33
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 34
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 35
    • 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.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 37
    • 38849183559 scopus 로고    scopus 로고
    • Sparse representation and Bayesian detection of genome copy number alterations from microarray data
    • Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, et al. (2008) Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics 24: 309-318.
    • (2008) Bioinformatics , vol.24 , pp. 309-318
    • Pique-Regi, R.1    Monso-Varona, J.2    Ortega, A.3    Seeger, R.C.4    Triche, T.J.5
  • 40
    • 79960036578 scopus 로고    scopus 로고
    • Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
    • Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, et al. (2011) Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475: 101-105.
    • (2011) Nature , vol.475 , pp. 101-105
    • Puente, X.S.1    Pinyol, M.2    Quesada, V.3    Conde, L.4    Ordonez, G.R.5
  • 41
    • 84870837088 scopus 로고    scopus 로고
    • The GEM mapper: fast, accurate and versatile alignment by filtration
    • Marco-Sola S, Sammeth M, Guigo R, Ribeca P (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods.
    • (2012) Nat Methods
    • Marco-Sola, S.1    Sammeth, M.2    Guigo, R.3    Ribeca, P.4
  • 43
    • 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 JO, Abyzov A, Mu XJ, Carriero N, Cayting P, et al. (2009) 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) Genome Biol , vol.10
    • Korbel, J.O.1    Abyzov, A.2    Mu, X.J.3    Carriero, N.4    Cayting, P.5
  • 44
    • 84861628224 scopus 로고    scopus 로고
    • Detectable clonal mosaicism and its relationship to aging and cancer
    • Jacobs KB, Yeager M, Zhou W, Wacholder S, Wang Z, et al. (2012) Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet 44: 651-658.
    • (2012) Nat Genet , vol.44 , pp. 651-658
    • Jacobs, K.B.1    Yeager, M.2    Zhou, W.3    Wacholder, S.4    Wang, Z.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.