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Volumn 30, Issue 18, 2014, Pages 2576-2583

CLImAT: Accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ANEUPLOIDY; ARTICLE; COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA SEQUENCE; GENE FREQUENCY; GENETICS; GENOMICS; HETEROZYGOSITY LOSS; HUMAN; METHODOLOGY; TRIPLE NEGATIVE BREAST CANCER;

EID: 84907525236     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu346     Document Type: Article
Times cited : (41)

References (36)
  • 1
    • 0042166174 scopus 로고    scopus 로고
    • Chromosome aberrations in solid tumors
    • Albertson, D.G. et al. (2003) Chromosome aberrations in solid tumors. Nat. Genet., 34, 369-376.
    • (2003) Nat. Genet. , vol.34 , pp. 369-376
    • Albertson, D.G.1
  • 2
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 3
    • 77249123407 scopus 로고    scopus 로고
    • Signatures of mutation and selection in the cancer genome
    • Bignell, G.R. et al. (2010) Signatures of mutation and selection in the cancer genome. Nature, 463, 893-898.
    • (2010) Nature , vol.463 , pp. 893-898
    • Bignell, G.R.1
  • 4
    • 78651430230 scopus 로고    scopus 로고
    • Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
    • Boeva, V. et al. (2011) Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics, 27, 268-269.
    • (2011) Bioinformatics , vol.27 , pp. 268-269
    • Boeva, V.1
  • 5
    • 84856561659 scopus 로고    scopus 로고
    • Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
    • Boeva, V. et al. (2012) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics, 28, 423-425.
    • (2012) Bioinformatics , vol.28 , pp. 423-425
    • Boeva, V.1
  • 6
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1
  • 7
    • 77749279754 scopus 로고    scopus 로고
    • High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset
    • Caren, H. et al. (2010) High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc. Natl Acad. Sci. USA, 107, 4323-4328.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 4323-4328
    • Caren, H.1
  • 8
    • 84860782006 scopus 로고    scopus 로고
    • Absolute quantification of somatic DNA alterations in human cancer
    • Carter, S.L. et al. (2012) Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol., 30, 413-421.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 413-421
    • Carter, S.L.1
  • 9
    • 84875185177 scopus 로고    scopus 로고
    • Comparative studies of copy number variation detection methods for next-generation sequencing technologies
    • Duan, J. et al. (2013) Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One, 8, e59128.
    • (2013) PLoS One , vol.8 , pp. e59128
    • Duan, J.1
  • 10
    • 77951957381 scopus 로고    scopus 로고
    • SNVMix: Predicting single nucleotide variants from next-generation sequencing of tumors
    • Goya, R. et al. (2010) SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics, 26, 730-736.
    • (2010) Bioinformatics , vol.26 , pp. 730-736
    • Goya, R.1
  • 11
    • 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
    • Gusnanto, A. et al. (2012) Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics, 28, 40-47.
    • (2012) Bioinformatics , vol.28 , pp. 40-47
    • Gusnanto, A.1
  • 12
    • 84867164956 scopus 로고    scopus 로고
    • Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
    • Ha, G. et al. (2012) Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res., 22, 1995-2007.
    • (2012) Genome Res. , vol.22 , pp. 1995-2007
    • Ha, G.1
  • 13
    • 84883063871 scopus 로고    scopus 로고
    • Virmid: Accurate detection of somatic mutations with sample impurity inference
    • Kim, S. et al. (2013) Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol., 14, R90.
    • (2013) Genome Biol. , vol.14 , pp. R90
    • Kim, S.1
  • 14
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1
  • 15
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and 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
  • 16
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 17
    • 79960268207 scopus 로고    scopus 로고
    • GPHMM: An integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
    • Li, A. et al. (2011) GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Res., 39, 4928-4941.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4928-4941
    • Li, A.1
  • 18
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis, E.R. (2008) Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet., 9, 387-402.
    • (2008) Annu. Rev. Genomics Hum. Genet. , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 19
    • 84875341635 scopus 로고    scopus 로고
    • Patchwork: Allele-specific copy number analysis of whole genome sequenced tumor tissue
    • Mayrhofer, M. et al. (2013) Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue. Genome Biol., 14, R24.
    • (2013) Genome Biol. , vol.14 , pp. R24
    • Mayrhofer, M.1
  • 20
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-the next generation
    • Metzker, M.L. (2009) Sequencing technologies-the next generation. Nat. Rev. Genet., 11, 31-46.
    • (2009) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 21
    • 53649088131 scopus 로고    scopus 로고
    • Applications of next-generation sequencing technologies in functional genomics
    • Morozova, O. and Marra, M.A. (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics, 92, 255-264.
    • (2008) Genomics , vol.92 , pp. 255-264
    • Morozova, O.1    Marra, M.A.2
  • 22
    • 84880934918 scopus 로고    scopus 로고
    • THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
    • Oesper, L. et al. (2013) THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol., 14, R80.
    • (2013) Genome Biol. , vol.14 , pp. R80
    • Oesper, L.1
  • 23
    • 57049089497 scopus 로고    scopus 로고
    • Experimental design and data analysis for array comparative gen-omic hybridization
    • Park, P.J. (2008) Experimental design and data analysis for array comparative gen-omic hybridization. Cancer Invest., 26, 923-928.
    • (2008) Cancer Invest. , vol.26 , pp. 923-928
    • Park, P.J.1
  • 24
    • 33748272115 scopus 로고    scopus 로고
    • High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
    • Peiffer, D.A. et al. (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res., 16, 1136-1148.
    • (2006) Genome Res. , vol.16 , pp. 1136-1148
    • Peiffer, D.A.1
  • 25
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner, L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
    • (1989) Proc. IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 26
    • 80053446554 scopus 로고    scopus 로고
    • Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
    • Sathirapongsasuti, J.F. et al. (2011) Exome sequencing-based copy-number variation and loss of heterozygosity detection: exomeCNV. Bioinformatics, 27, 2648-2654.
    • (2011) Bioinformatics , vol.27 , pp. 2648-2654
    • Sathirapongsasuti, J.F.1
  • 27
    • 79952292177 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • Schuster, S.C. (2007) Next-generation sequencing transforms today's biology. Nature, 200, 8.
    • (2007) Nature , vol.200 , pp. 8
    • Schuster, S.C.1
  • 28
    • 84862526929 scopus 로고    scopus 로고
    • The clonal and mutational evolution spectrum of primary triple-negative breast cancers
    • Shah, S.P. et al. (2012) The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature, 486, 395-399.
    • (2012) Nature , vol.486 , pp. 395-399
    • Shah, S.P.1
  • 29
    • 0035173378 scopus 로고    scopus 로고
    • DbSNP: The NCBI database of genetic variation
    • Sherry, S.T. et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 308-311
    • Sherry, S.T.1
  • 30
    • 72949119310 scopus 로고    scopus 로고
    • Complex landscapes of somatic rearrangement in human breast cancer genomes
    • Stephens, P.J. et al. (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462, 1005-1010.
    • (2009) Nature , vol.462 , pp. 1005-1010
    • Stephens, P.J.1
  • 31
    • 64749094310 scopus 로고    scopus 로고
    • The cancer genome
    • Stratton, M.R. et al. (2009) The cancer genome. Nature, 458, 719-724.
    • (2009) Nature , vol.458 , pp. 719-724
    • Stratton, M.R.1
  • 32
    • 0034307169 scopus 로고    scopus 로고
    • An approach to analysis of large-scale correlations between genome changes and clinical endpoints in ovarian cancer
    • Suzuki, S. et al. (2000) An approach to analysis of large-scale correlations between genome changes and clinical endpoints in ovarian cancer. Cancer Res., 60, 5382-5385.
    • (2000) Cancer Res. , vol.60 , pp. 5382-5385
    • Suzuki, S.1
  • 33
    • 78049248432 scopus 로고    scopus 로고
    • Allele-specific copy number analysis of tumors
    • Van Loo, P. et al. (2010) Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA, 107, 16910-16915.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 16910-16915
    • Van Loo, P.1
  • 34
    • 81755172942 scopus 로고    scopus 로고
    • Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
    • Xi, R. et al. (2011) Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc. Natl Acad. Sci. USA, 108, E1128-E1136.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. E1128-E1136
    • Xi, R.1
  • 35
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon, S. et al. (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
  • 36
    • 79953306829 scopus 로고    scopus 로고
    • The telomerase inhibitor PinX1 is a major haploinsufficient tumor suppressor essential for chromosome stability in mice
    • Zhou, X.Z. et al. (2011) The telomerase inhibitor PinX1 is a major haploinsufficient tumor suppressor essential for chromosome stability in mice. J. Clin. Invest., 121, 1266.
    • (2011) J. Clin. Invest. , vol.121 , pp. 1266
    • Zhou, X.Z.1


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