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Volumn 15, Issue 1, 2014, Pages

SeqCNA: An R package for DNA copy number analysis in cancer using high-throughput sequencing

Author keywords

Bioconductor; Cancer; Copy number; High throughput sequencing; R

Indexed keywords

ARTICLE; CANCER GENETICS; COPY NUMBER ALTERATION; COPY NUMBER VARIATION; DNA BASE COMPOSITION; GENE MAPPING; GENETIC ANALYSIS; GENETIC CORRELATION; GENETIC DATABASE; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; INTERMETHOD COMPARISON; QUALITY CONTROL; SEQUENCE ANALYSIS;

EID: 84899481863     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-178     Document Type: Article
Times cited : (10)

References (34)
  • 1
    • 64749094310 scopus 로고    scopus 로고
    • The cancer genome
    • 10.1038/nature07943, 2821689, 19360079
    • Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009, 458(7239):719-724. 10.1038/nature07943, 2821689, 19360079.
    • (2009) Nature , vol.458 , Issue.7239 , pp. 719-724
    • Stratton, M.R.1    Campbell, P.J.2    Futreal, P.A.3
  • 3
    • 83055168377 scopus 로고    scopus 로고
    • Relating cnvs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions
    • 10.1101/gr.122614.111, 3227091, 21862627
    • Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO. Relating cnvs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Res 2011, 21(12):2004-2013. 10.1101/gr.122614.111, 3227091, 21862627.
    • (2011) Genome Res , vol.21 , Issue.12 , pp. 2004-2013
    • Schlattl, A.1    Anders, S.2    Waszak, S.M.3    Huber, W.4    Korbel, J.O.5
  • 4
    • 33845768982 scopus 로고    scopus 로고
    • Dosage compensation: the beginning and end of generalization
    • 10.1038/nrg2013, 17173057
    • Straub T, Becker PB. Dosage compensation: the beginning and end of generalization. Nat Rev Genet 2007, 8(1):47-57. 10.1038/nrg2013, 17173057.
    • (2007) Nat Rev Genet , vol.8 , Issue.1 , pp. 47-57
    • Straub, T.1    Becker, P.B.2
  • 6
    • 48949115115 scopus 로고    scopus 로고
    • Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects
    • 10.1016/j.tig.2008.05.005, 18585818
    • Veitia RA, Bottani S, Birchler JA. Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet 2008, 24(8):390-397. 10.1016/j.tig.2008.05.005, 18585818.
    • (2008) Trends Genet , vol.24 , Issue.8 , pp. 390-397
    • Veitia, R.A.1    Bottani, S.2    Birchler, J.A.3
  • 7
    • 78049443323 scopus 로고    scopus 로고
    • Proteomic changes resulting from gene copy number variations in cancer cells
    • Geiger T, Cox J, Mann M. Proteomic changes resulting from gene copy number variations in cancer cells. PLoS Genet 2010, 6(9):1001090.
    • (2010) PLoS Genet , vol.6 , Issue.9 , pp. 1001090
    • Geiger, T.1    Cox, J.2    Mann, M.3
  • 9
    • 80053908833 scopus 로고    scopus 로고
    • Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over
    • 10.1016/j.ajhg.2011.09.009, 3188830, 21981782
    • Liu P, Lacaria M, Zhang F, Withers M, Hastings P, Lupski JR. Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over. Am J Hum Genet 2011, 89(4):580-588. 10.1016/j.ajhg.2011.09.009, 3188830, 21981782.
    • (2011) Am J Hum Genet , vol.89 , Issue.4 , pp. 580-588
    • Liu, P.1    Lacaria, M.2    Zhang, F.3    Withers, M.4    Hastings, P.5    Lupski, J.R.6
  • 10
    • 84855185866 scopus 로고    scopus 로고
    • Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data
    • 10.1093/bioinformatics/btr593, 22039209
    • Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 2012, 28(1):40-47. 10.1093/bioinformatics/btr593, 22039209.
    • (2012) Bioinformatics , vol.28 , Issue.1 , pp. 40-47
    • Gusnanto, A.1    Wood, H.M.2    Pawitan, Y.3    Rabbitts, P.4    Berri, S.5
  • 11
    • 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(9):1586-1592. 10.1101/gr.092981.109, 2752127, 19657104.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1586-1592
    • Yoon, S.1    Xuan, Z.2    Makarov, V.3    Ye, K.4    Sebat, J.5
  • 12
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput dna sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput dna sequencing. Nucleic Acids Res 2008, 36(16):105-105.
    • (2008) Nucleic Acids Res , vol.36 , Issue.16 , pp. 105-105
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 13
    • 84876082103 scopus 로고    scopus 로고
    • Effective normalization for copy number variation detection from whole genome sequencing
    • 10.1186/1471-2164-13-S6-S16, 3315736, 22235840
    • Janevski A, Varadan V, Kamalakaran S, Banerjee N, Dimitrova N.Effective normalization for copy number variation detection from whole genome sequencing. BMC Genomics 2012, 13(Suppl 6):16. 10.1186/1471-2164-13-S6-S16, 3315736, 22235840.
    • (2012) BMC Genomics , vol.13 , Issue.SUPPL. 6 , pp. 16
    • Janevski, A.1    Varadan, V.2    Kamalakaran, S.3    Banerjee, N.4    Dimitrova, N.5
  • 14
    • 78651430230 scopus 로고    scopus 로고
    • Control-free calling of copy number alterations in deep-sequencing data using gc-content normalization
    • 10.1093/bioinformatics/btq635, 3018818, 21081509
    • Boeva V, Zinovyev A, Bleakley K, Vert J-P, Janoueix-Lerosey I, Delattre O, Barillot E. Control-free calling of copy number alterations in deep-sequencing data using gc-content normalization. Bioinformatics 2011, 27(2):268-269. 10.1093/bioinformatics/btq635, 3018818, 21081509.
    • (2011) Bioinformatics , vol.27 , Issue.2 , pp. 268-269
    • Boeva, V.1    Zinovyev, A.2    Bleakley, K.3    Vert, J.-P.4    Janoueix-Lerosey, I.5    Delattre, O.6    Barillot, E.7
  • 15
    • 84870816675 scopus 로고    scopus 로고
    • Bioconductor
    • Bioconductor. [http://bioconductor.org/].
  • 16
    • 12344259648 scopus 로고    scopus 로고
    • Analysis of array cgh data: from signal ratio to gain and loss of dna regions
    • 10.1093/bioinformatics/bth418, 15381628
    • Stransky N, Thiery J-P, Radvanyi F, Barillot E, Hupé P Analysis of array cgh data: from signal ratio to gain and loss of dna regions. Bioinformatics 2004, 20(18):3413-3422. 10.1093/bioinformatics/bth418, 15381628, Hupé P.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3413-3422
    • Stransky, N.1    Thiery, J.-P.2    Radvanyi, F.3    Barillot, E.4    Hupé, P.5
  • 17
    • 33746277229 scopus 로고    scopus 로고
    • The package adehabitat for the r software: tool for the analysis of space and habitat use by animals
    • Calenge C. The package adehabitat for the r software: tool for the analysis of space and habitat use by animals. Ecol Model 2006, 197:1035.
    • (2006) Ecol Model , vol.197 , pp. 1035
    • Calenge, C.1
  • 18
    • 59249098545 scopus 로고    scopus 로고
    • Snow: A parallel computing framework for the r system
    • Tierney L, Rossini AJ, Li N. Snow: A parallel computing framework for the r system. Int J Parallel Program 2009, 37(1):78-90.
    • (2009) Int J Parallel Program , vol.37 , Issue.1 , pp. 78-90
    • Tierney, L.1    Rossini, A.J.2    Li, N.3
  • 19
    • 84870486790 scopus 로고    scopus 로고
    • The Comprehensive R Archive Network
    • The Comprehensive R Archive Network. [http://cran.r-project.org/].
  • 21
    • 84868016827 scopus 로고    scopus 로고
    • Statistical challenges associated with detecting copy number variations with next-generation sequencing
    • 10.1093/bioinformatics/bts535, 22942022
    • Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 2012, 28(21):2711-2718. 10.1093/bioinformatics/bts535, 22942022.
    • (2012) Bioinformatics , vol.28 , Issue.21 , pp. 2711-2718
    • Teo, S.M.1    Pawitan, Y.2    Ku, C.S.3    Chia, K.S.4    Salim, A.5
  • 23
    • 84857170661 scopus 로고    scopus 로고
    • Read count approach for dna copy number variants detection
    • 10.1093/bioinformatics/btr707, 22199393
    • Magi A, Tattini L, Pippucci T, Torricelli F, Benelli M. Read count approach for dna copy number variants detection. Bioinformatics 2012, 28(4):470-478. 10.1093/bioinformatics/btr707, 22199393.
    • (2012) Bioinformatics , vol.28 , Issue.4 , pp. 470-478
    • Magi, A.1    Tattini, L.2    Pippucci, T.3    Torricelli, F.4    Benelli, M.5
  • 25
    • 84899471350 scopus 로고    scopus 로고
    • ENCODE Mapability Data
    • ENCODE Mapability Data. [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/].
  • 26
    • 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 AE, 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(6):974-984. 10.1101/gr.114876.110, 3106330, 21324876.
    • (2011) Genome Res , vol.21 , Issue.6 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 27
    • 84890189765 scopus 로고    scopus 로고
    • Oncosnp-seq: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes
    • 10.1093/bioinformatics/btt416, 23926227
    • Yau C.Oncosnp-seq: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes. Bioinformatics 2013, 29(19):2482-2484. 10.1093/bioinformatics/btt416, 23926227.
    • (2013) Bioinformatics , vol.29 , Issue.19 , pp. 2482-2484
    • Yau, C.1
  • 28
    • 84875341635 scopus 로고    scopus 로고
    • Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue
    • Mayrhofer M, DiLorenzo S, Isaksson A. Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue. Genome Biol 2013, 14:24.
    • (2013) Genome Biol , vol.14 , pp. 24
    • Mayrhofer, M.1    DiLorenzo, S.2    Isaksson, A.3
  • 29
    • 84864751097 scopus 로고    scopus 로고
    • Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data
    • 10.1186/1471-2105-13-192, 3472297, 22870940
    • Mosén-Ansorena D, Aransay A, Rodríguez-Ezpeleta N.Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. BMC Bioinformatics 2012, 13(1):192. 10.1186/1471-2105-13-192, 3472297, 22870940.
    • (2012) BMC Bioinformatics , vol.13 , Issue.1 , pp. 192
    • Mosén-Ansorena, D.1    Aransay, A.2    Rodríguez-Ezpeleta, N.3
  • 30
    • 76249097734 scopus 로고    scopus 로고
    • Genome alteration print (gap): a tool to visualize and mine complex cancer genomic profiles obtained by snp arrays
    • Popova T, Stoppa-Lyonnet D, Rigaill G, Barillot E, Stern MH, Manié E.Genome alteration print (gap): a tool to visualize and mine complex cancer genomic profiles obtained by snp arrays. Genome Biol 2009, 10(11):128-128. Manié E.
    • (2009) Genome Biol , vol.10 , Issue.11 , pp. 128-128
    • Popova, T.1    Stoppa-Lyonnet, D.2    Rigaill, G.3    Barillot, E.4    Stern, M.H.5    Manié, E.6


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