메뉴 건너뛰기




Volumn 30, Issue 6, 2014, Pages 768-774

WaveCNV: Allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALLELE; ANEUPLOIDY; ANIMAL; ARTICLE; COMPUTER PROGRAM; COPY NUMBER VARIATION; DNA SEQUENCE; DRUG SCREENING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; MOUSE; NEOPLASM;

EID: 84897853363     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt611     Document Type: Article
Times cited : (14)

References (25)
  • 1
    • 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. et al. (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
  • 2
    • 84861033754 scopus 로고    scopus 로고
    • Genome-wide copy number analysis of single cells
    • Baslan, T. et al. (2012) Genome-wide copy number analysis of single cells. Nat. Protoc., 7, 1024-1041.
    • (2012) Nat. Protoc. , vol.7 , pp. 1024-1041
    • Baslan, T.1
  • 3
    • 84869091997 scopus 로고    scopus 로고
    • Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
    • Biankin, A.V. et al. (2012) Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature, 491, 399-405.
    • (2012) Nature , vol.491 , pp. 399-405
    • Biankin, A.V.1
  • 4
    • 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
  • 5
    • 0002001578 scopus 로고
    • Translation-invariant de-noising
    • In: Antoniadis, A. and Oppenheim, G. (eds). Springer-Verlag, New York
    • Coifman, R.R. and Donoho, D.L. (1995) Translation-invariant de-noising. In: Antoniadis, A. and Oppenheim, G. (eds) Wavelets and Statistics. Springer-Verlag, New York.
    • (1995) Wavelets and Statistics
    • Coifman, R.R.1    Donoho, D.L.2
  • 6
    • 84860645682 scopus 로고    scopus 로고
    • Xenome-A tool for classifying reads from xenograft samples
    • Conway, T. et al. (2012) Xenome-a tool for classifying reads from xenograft samples. Bioinformatics, 28, i172-i178.
    • (2012) Bioinformatics , vol.28
    • Conway, T.1
  • 7
    • 79957600437 scopus 로고    scopus 로고
    • Development of an orthotopic human pancreatic cancer xenograft model using ultrasound guided injection of cells
    • Huynh, A.S. et al. (2011) Development of an orthotopic human pancreatic cancer xenograft model using ultrasound guided injection of cells. PLoS One, 6, e20330.
    • (2011) PLoS One , vol.6
    • Huynh, A.S.1
  • 8
    • 79951748341 scopus 로고    scopus 로고
    • CNAseg-A novel framework for identification of copy number changes in cancer from second-generation sequencing data
    • Ivakhno, S. et al. (2010) CNAseg-a novel framework for identification of copy number changes in cancer from second-generation sequencing data. Bioinformatics, 26, 3051-3058.
    • (2010) Bioinformatics , vol.26 , pp. 3051-3058
    • Ivakhno, S.1
  • 9
    • 77955635446 scopus 로고    scopus 로고
    • RSW-seq: Algorithm for detection of copy number alterations in deep sequencing data
    • Kim, T.M. et al. (2010) rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. BMC Bioinformatics, 11, 432.
    • (2010) BMC Bioinformatics , vol.11 , pp. 432
    • Kim, T.M.1
  • 10
    • 84861400043 scopus 로고    scopus 로고
    • Cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
    • Klambauer, G. et al. (2012) cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res., 40, e69.
    • (2012) Nucleic Acids Res. , vol.40
    • Klambauer, G.1
  • 11
    • 33847133505 scopus 로고    scopus 로고
    • A comparison of continuous wavelet transform and modulus maxima analysis of characteristic ECG features
    • Legarreta, I.R. et al. (2005) A comparison of continuous wavelet transform and modulus maxima analysis of characteristic ECG features. Comput. Cardiol., 32, 755-758.
    • (2005) Comput. Cardiol. , vol.32 , pp. 755-758
    • Legarreta, I.R.1
  • 12
    • 79961202047 scopus 로고    scopus 로고
    • Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm
    • Magi, A. et al. (2011) Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res., 39, e65.
    • (2011) Nucleic Acids Res. , vol.39
    • Magi, A.1
  • 14
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing
    • Medvedev, P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
    • (2009) Nat. Methods , vol.6
    • Medvedev, P.1
  • 15
    • 79551621409 scopus 로고    scopus 로고
    • ReadDepth: A parallel R package for detecting copy number alterations from short sequencing reads
    • Miller, C.A. et al. (2011) ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One, 6, e16327.
    • (2011) PLoS One , vol.6
    • Miller, C.A.1
  • 16
    • 34347254640 scopus 로고    scopus 로고
    • Establishment of human tumor xenografts in immunodeficient mice
    • Morton, C.L. and Houghton, P.J. (2007) Establishment of human tumor xenografts in immunodeficient mice. Nat. Protoc., 2, 247-250.
    • (2007) Nat. Protoc. , vol.2 , pp. 247-250
    • Morton, C.L.1    Houghton, P.J.2
  • 17
    • 79953766940 scopus 로고    scopus 로고
    • Tumour evolution inferred by single-cell sequencing
    • Navin, N. et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472, 90-94.
    • (2011) Nature , vol.472 , pp. 90-94
    • Navin, N.1
  • 18
    • 84866700697 scopus 로고    scopus 로고
    • Qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles
    • Song, S. et al. (2012) qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One, 7, e45835.
    • (2012) PLoS One , vol.7
    • Song, S.1
  • 19
    • 70449418416 scopus 로고    scopus 로고
    • Integrated study of copy number states and genotype calls using high-density SNP arrays
    • Sun, W. et al. (2009) Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res., 37, 5365-5377.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5365-5377
    • Sun, W.1
  • 20
    • 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
  • 21
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    • Wang, K. et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res., 17, 1665-1674.
    • (2007) Genome Res. , vol.17 , pp. 1665-1674
    • Wang, K.1
  • 22
    • 78649646546 scopus 로고    scopus 로고
    • Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity
    • Waszak, S.M. et al. (2010) Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput. Biol., 6, e1000988.
    • (2010) PLoS Comput. Biol. , vol.6
    • Waszak, S.M.1
  • 23
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing
    • Xie, C. and Tammi, M.T. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10, 80.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.T.2
  • 24
    • 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
    • Yau, C. (2013) OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes. Bioinformatics, 29, 2482-2484.
    • (2013) Bioinformatics , vol.29 , pp. 2482-2484
    • Yau, C.1
  • 25
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.