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Volumn 8, Issue 12, 2013, Pages

Softsearch: Integration of multiple sequence features to identify breakpoints of structural variations

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; EXOME; GENETIC ANALYSIS; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOME; HUMAN; NEXT GENERATION SEQUENCING; SEQUENCE ALIGNMENT; SIMULATION; TUMOR SUPPRESSOR GENE; VALIDATION PROCESS;

EID: 84892656321     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083356     Document Type: Article
Times cited : (33)

References (19)
  • 1
    • 17344365851 scopus 로고    scopus 로고
    • Genetic Heterogeneity and Penetrance Analysis of the BRCA1 and BRCA2 Genes in Breast Cancer Families
    • doi:10.1086/301749
    • Ford D, Easton DF, Stratton M, Narod S, Goldgar D et al. (1998) Genetic Heterogeneity and Penetrance Analysis of the BRCA1 and BRCA2 Genes in Breast Cancer Families. American Journal of Human Genetics 62: 676-689. doi:10.1086/301749.
    • (1998) American Journal of Human Genetics , vol.62 , pp. 676-689
    • Ford, D.1    Easton, D.F.2    Stratton, M.3    Narod, S.4    Goldgar, D.5
  • 2
    • 33645100274 scopus 로고    scopus 로고
    • Large genomic deletions inactivate the BRCA2 gene in breast cancer families
    • doi:10.1136/jmg.2005.032789. PubMed: 16199546
    • Agata S, Dalla Palma M, Callegaro M, Scaini MC, Menin C et al. (2005) Large genomic deletions inactivate the BRCA2 gene in breast cancer families. J Med Genet 42: e64. doi:10.1136/jmg.2005.032789. PubMed: 16199546.
    • (2005) J Med Genet , vol.42
    • Agata, S.1    Dalla Palma, M.2    Callegaro, M.3    Scaini, M.C.4    Menin, C.5
  • 4
    • 0038364017 scopus 로고    scopus 로고
    • Genomic rearrangements account for more than one-third of the BRCA1 mutations in northern Italian breast/ovarian cancer families
    • doi:10.1093/hmg/ddg120. PubMed: 12700174
    • Montagna M, Palma MD, Menin C, Agata S, De Nicolo A et al. (2003) Genomic rearrangements account for more than one-third of the BRCA1 mutations in northern Italian breast/ovarian cancer families. Hum Mol Genet 12: 1055-1061. doi:10.1093/hmg/ddg120. PubMed: 12700174.
    • (2003) Hum Mol Genet , vol.12 , pp. 1055-1061
    • Montagna, M.1    Palma, M.D.2    Menin, C.3    Agata, S.4    De Nicolo, A.5
  • 5
    • 52049088505 scopus 로고    scopus 로고
    • The Relative Contribution of Point Mutations and Genomic Rearrangements in BRCA1 and BRCA2 in High-Risk Breast Cancer Families
    • doi:10.1158/0008-5472.CAN-08-0599. PubMed: 18703817
    • Palma MD, Domchek SM, Stopfer J, Erlichman J, Siegfried JD et al. (2008) The Relative Contribution of Point Mutations and Genomic Rearrangements in BRCA1 and BRCA2 in High-Risk Breast Cancer Families. Cancer Res 68: 7006-7014. doi:10.1158/0008-5472.CAN-08-0599. PubMed: 18703817.
    • (2008) Cancer Res , vol.68 , pp. 7006-7014
    • Palma, M.D.1    Domchek, S.M.2    Stopfer, J.3    Erlichman, J.4    Siegfried, J.D.5
  • 6
    • 33645106126 scopus 로고    scopus 로고
    • Large genomic rearrangements of both BRCA2 and BRCA1 are a feature of the inherited breast/ovarian cancer phenotype in selected families
    • doi:10.1136/jmg.2004.027961. PubMed: 15863663
    • Woodward AM, Davis TA, Silva AGS, Kirk JA, Leary JA (2005) Large genomic rearrangements of both BRCA2 and BRCA1 are a feature of the inherited breast/ovarian cancer phenotype in selected families. J Med Genet 42: e31. doi:10.1136/jmg.2004.027961. PubMed: 15863663.
    • (2005) J Med Genet , vol.42
    • Woodward, A.M.1    Davis, T.A.2    Silva, A.G.S.3    Kirk, J.A.4    Leary, J.A.5
  • 7
    • 79955004110 scopus 로고    scopus 로고
    • Detecting structural variations in the human genome using next generation sequencing
    • doi:10.1093/bfgp/elq025. PubMed: 21216738
    • Xi R, Kim T-M, Park PJ (2010) Detecting structural variations in the human genome using next generation sequencing. Brief Funct Genomics 9: 405-415. doi:10.1093/bfgp/elq025. PubMed: 21216738.
    • (2010) Brief Funct Genomics , vol.9 , pp. 405-415
    • Xi, R.1    Kim, T.-M.2    Park, P.J.3
  • 8
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • doi:10.1101/gr.114876.110. PubMed: 21324876
    • 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. doi:10.1101/gr.114876.110. PubMed: 21324876.
    • (2011) Genome Res , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 9
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
    • doi:10.1038/nmeth.1363. PubMed: 19668202
    • 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. doi:10.1038/nmeth.1363. PubMed: 19668202.
    • (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
  • 10
    • 77951860138 scopus 로고    scopus 로고
    • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • doi:10.1101/gr.102970.109. PubMed: 20308636
    • 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. doi:10.1101/gr.102970.109. PubMed: 20308636.
    • (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
  • 11
    • 84856409929 scopus 로고    scopus 로고
    • Detection of structural variants and indels within exome data
    • PubMed: 22179552
    • Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L et al. (2012) Detection of structural variants and indels within exome data. Nat Methods 9: 176-178. PubMed: 22179552.
    • (2012) Nat Methods , vol.9 , pp. 176-178
    • Karakoc, E.1    Alkan, C.2    O'Roak, B.J.3    Dennis, M.Y.4    Vives, L.5
  • 12
    • 79961007031 scopus 로고    scopus 로고
    • CREST maps somatic structural variation in cancer genomes with base-pair resolution
    • doi:10.1038/nmeth.1628. PubMed: 21666668
    • 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. doi:10.1038/nmeth.1628. PubMed: 21666668.
    • (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
  • 13
    • 82255164279 scopus 로고    scopus 로고
    • SVseq: An approach for detecting exact breakpoints of deletions with low-coverage sequence data
    • doi:10.1093/bioinformatics/btr563. PubMed: 21994222
    • Zhang J, Wu Y (2011) SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data. Bioinformatics 27: 3228-3234. doi:10.1093/bioinformatics/btr563. PubMed: 21994222.
    • (2011) Bioinformatics , vol.27 , pp. 3228-3234
    • Zhang, J.1    Wu, Y.2
  • 14
    • 84870460670 scopus 로고    scopus 로고
    • PRISM: Pair read informed split read mapping for base-pair level detection of insertion, deletion and structural variants
    • Jiang Y, Wang Y, Brudno M (2012) PRISM: Pair read informed split read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics.
    • (2012) Bioinformatics
    • Jiang, Y.1    Wang, Y.2    Brudno, M.3
  • 15
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: Structural variant discovery by integrated paired-end and split-read analysis
    • doi:10.1093/bioinformatics/bts378. PubMed: 22962449
    • Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28: i333-i339. doi:10.1093/bioinformatics/bts378. PubMed: 22962449.
    • (2012) Bioinformatics , vol.28
    • Rausch, T.1    Zichner, T.2    Schlattl, A.3    Stütz, A.M.4    Benes, V.5
  • 16
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • doi:10.1093/bioinformatics/btp352. PubMed: 19505943
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352. PubMed: 19505943.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5
  • 17
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • doi:10.1093/bioinformatics/btq033. PubMed: 20110278
    • Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842. doi:10.1093/ bioinformatics/btq033. PubMed: 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 18
    • 84975804424 scopus 로고    scopus 로고
    • Mapping copy number variation by population-scale genome sequencing
    • doi:10.1038/nature09708. PubMed: 21293372
    • 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. doi:10.1038/nature09708. PubMed: 21293372.
    • (2011) Nature , vol.470 , pp. 59-65
    • Mills, R.E.1    Walter, K.2    Stewart, C.3    Handsaker, R.E.4    Chen, K.5
  • 19
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
    • doi:10.1038/nmeth.1363. PubMed: 19668202
    • 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. doi:10.1038/nmeth.1363. PubMed: 19668202.
    • (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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.