메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages 308-

Detection of recurrent copy number alterations in the genome: Taking among-subject heterogeneity seriously

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INTERPRETATION; COPY-NUMBER ALTERATIONS; GENOMIC REGIONS; INTERPRETABILITY; POPULATION HETEROGENEITY; RESEARCH QUESTIONS; RETURN PROBABILITIES; TWO PARAMETER;

EID: 70449358724     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-308     Document Type: Article
Times cited : (11)

References (61)
  • 4
    • 62549158266 scopus 로고    scopus 로고
    • Computational methods for identification of recurrent copy number alteration patterns by array CGH
    • Shah SP. Computational methods for identification of recurrent copy number alteration patterns by array CGH. Cytogenetic and genome research 2008, 123(1-4):343-351.
    • (2008) Cytogenetic and genome research , vol.123 , Issue.1-4 , pp. 343-351
    • Shah, S.P.1
  • 5
    • 34347361618 scopus 로고    scopus 로고
    • Copy number variations and clinical cytogenetic diagnosis of constitutional disorders
    • Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nature Genetics 2007, 39:S48-S54.
    • (2007) Nature Genetics , vol.39
    • Lee, C.1    Iafrate, A.J.2    Brothman, A.R.3
  • 7
    • 34347349069 scopus 로고    scopus 로고
    • Genomic rearrangements and sporadic disease
    • Lupski JR. Genomic rearrangements and sporadic disease. Nature Genetics 2007, 39:S43-S47.
    • (2007) Nature Genetics , vol.39
    • Lupski, J.R.1
  • 8
    • 34347353237 scopus 로고    scopus 로고
    • Copy-number variation and association studies of human disease
    • McCarroll SA, Altshuler DM. Copy-number variation and association studies of human disease. Nat Genet 2007, 39(7 Suppl):S37-S42.
    • (2007) Nat Genet , vol.39 , Issue.7 SUPPL
    • McCarroll, S.A.1    Altshuler, D.M.2
  • 9
    • 34447569298 scopus 로고    scopus 로고
    • Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability
    • Beckmann JS, Estivill X, Antonarakis SE. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 2007, 8(8):639-646.
    • (2007) Nat Rev Genet , vol.8 , Issue.8 , pp. 639-646
    • Beckmann, J.S.1    Estivill, X.2    Antonarakis, S.E.3
  • 10
    • 67650735159 scopus 로고    scopus 로고
    • Genomic copy number variation, human health, and disease
    • Wain LV, Armour JAA, Tobin MD. Genomic copy number variation, human health, and disease. Lancet 2009, 374:340-350.
    • (2009) Lancet , vol.374 , pp. 340-350
    • Wain, L.V.1    Armour, J.A.A.2    Tobin, M.D.3
  • 12
    • 34347339520 scopus 로고    scopus 로고
    • Methods and strategies for analyzing copy number variation using DNA microarrays
    • 2697494, 17597776
    • Carter NP. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 2007, 39(7 Suppl):S16-S21. 2697494, 17597776.
    • (2007) Nat Genet , vol.39 , Issue.7 SUPPL
    • Carter, N.P.1
  • 13
    • 67949091187 scopus 로고    scopus 로고
    • Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
    • 2715261, 19570852
    • Laframboise T. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucl Acids Res 2009, 37(13):4181-4193. 2715261, 19570852.
    • (2009) Nucl Acids Res , vol.37 , Issue.13 , pp. 4181-4193
    • Laframboise, T.1
  • 14
    • 32644441984 scopus 로고    scopus 로고
    • BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH)
    • 1356528, 16439806
    • Ylstra B, Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 2006, 34:445-450. 1356528, 16439806.
    • (2006) Nucleic Acids Res , vol.34 , pp. 445-450
    • Ylstra, B.1    Ijssel, P.2    Carvalho, B.3    Brakenhoff, R.H.4    Meijer, G.A.5
  • 15
    • 20044375763 scopus 로고    scopus 로고
    • Array comparative genomic hybridization and its application in cancer
    • Pinkel D, Albertson D. Array comparative genomic hybridization and its application in cancer. Nature Genetics 2005, 37(Supplement):S11-S17.
    • (2005) Nature Genetics , vol.37 , Issue.SUPPL.
    • Pinkel, D.1    Albertson, D.2
  • 16
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing
    • 2667514, 19267900
    • Xie C, Tammi M. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009, 10:80. 2667514, 19267900.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.2
  • 17
    • 46249087524 scopus 로고    scopus 로고
    • A robust framework for detecting structural variations in a genome
    • 2718654, 18586745
    • Lee S, Cheran E, Brudno M. A robust framework for detecting structural variations in a genome. Bioinformatics 2008, 24(13):i59-67. 2718654, 18586745.
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Lee, S.1    Cheran, E.2    Brudno, M.3
  • 19
    • 33748276243 scopus 로고    scopus 로고
    • STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
    • 1557772, 16899652
    • Diskin S, Eck T, Greshock J, Mosse Y, Naylor T, Stoeckert CJ, Weber B, Maris J, Grant G. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 2006, 16(9):1149-1158. 1557772, 16899652.
    • (2006) Genome Res , vol.16 , Issue.9 , pp. 1149-1158
    • Diskin, S.1    Eck, T.2    Greshock, J.3    Mosse, Y.4    Naylor, T.5    Stoeckert, C.J.6    Weber, B.7    Maris, J.8    Grant, G.9
  • 22
    • 27544483495 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
    • Lai WRR, Johnson MDD, Kucherlapati R, Park PJJ. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21:3763-3770.
    • (2005) Bioinformatics , vol.21 , pp. 3763-3770
    • Lai, W.R.R.1    Johnson, M.D.D.2    Kucherlapati, R.3    Park, P.J.J.4
  • 23
    • 27944455289 scopus 로고    scopus 로고
    • A comparison study: applying segmentation to array CGH data for downstream analyses
    • Willenbrock H, Fridlyand J. A comparison study: applying segmentation to array CGH data for downstream analyses. Bioinformatics 2005, 21:4084-4091.
    • (2005) Bioinformatics , vol.21 , pp. 4084-4091
    • Willenbrock, H.1    Fridlyand, J.2
  • 24
    • 34347342852 scopus 로고    scopus 로고
    • Flexible and accurate detection of genomic copy-number changes from aCGH
    • Rueda OM, Diaz-Uriarte R. Flexible and accurate detection of genomic copy-number changes from aCGH. PLoS Comput Biol 2007, 3(6):1115-1122.
    • (2007) PLoS Comput Biol , vol.3 , Issue.6 , pp. 1115-1122
    • Rueda, O.M.1    Diaz-Uriarte, R.2
  • 25
    • 38849187801 scopus 로고    scopus 로고
    • A response to Yu et al. 'A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array', BMC Bioinformatics 2007, 8: 145
    • 2222656, 17939873
    • Rueda OM, Diaz-Uriarte R. A response to Yu et al. 'A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array', BMC Bioinformatics 2007, 8: 145. BMC Bioinformatics 2007, 8:394+. 2222656, 17939873.
    • (2007) BMC Bioinformatics , vol.8
    • Rueda, O.M.1    Diaz-Uriarte, R.2
  • 26
    • 79551640512 scopus 로고    scopus 로고
    • Finding Recurrent Copy Number Alteration Regions: A Review of Methods
    • Rueda OM, Diaz-Uriarte R. Finding Recurrent Copy Number Alteration Regions: A Review of Methods. Current Bioinformatics 2009,
    • (2009) Current Bioinformatics
    • Rueda, O.M.1    Diaz-Uriarte, R.2
  • 29
    • 33847308540 scopus 로고    scopus 로고
    • Markers improve clustering of CGH data
    • Liu J, Ranka S, Kahveci T. Markers improve clustering of CGH data. Bioinformatics 2007, 23(4):450-457.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 450-457
    • Liu, J.1    Ranka, S.2    Kahveci, T.3
  • 31
    • 33645993906 scopus 로고    scopus 로고
    • Efficient calculation of interval scores for DNA copy number data analysis
    • Lipson D, Aumann Y, Ben-Dor A, Linial N, Yakhinim Z. Efficient calculation of interval scores for DNA copy number data analysis. J Comput Biol 2006, 13(2):215-228.
    • (2006) J Comput Biol , vol.13 , Issue.2 , pp. 215-228
    • Lipson, D.1    Aumann, Y.2    Ben-Dor, A.3    Linial, N.4    Yakhinim, Z.5
  • 32
    • 34547844126 scopus 로고    scopus 로고
    • Modeling recurrrent CNA copy number alterations in array CGH data
    • Shah S, Lam W, Ng R, Murphy K. Modeling recurrrent CNA copy number alterations in array CGH data. Bioinformatics 2007, 23(13):i450-i458.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Shah, S.1    Lam, W.2    Ng, R.3    Murphy, K.4
  • 33
    • 34548452229 scopus 로고    scopus 로고
    • Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays
    • 1950957,1950957, 17722985
    • Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ, Grant GR. Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays. PLoS Genetics 2007, 3(8):e143+. 1950957,1950957, 17722985.
    • (2007) PLoS Genetics , vol.3 , Issue.8
    • Guttman, M.1    Mies, C.2    Dudycz-Sulicz, K.3    Diskin, S.J.4    Baldwin, D.A.5    Stoeckert, C.J.6    Grant, G.R.7
  • 36
    • 39149107114 scopus 로고    scopus 로고
    • Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data
    • 2241875, 18187509
    • Klijn C, Holstege H, de Ridder J, Liu X, Reinders M, Jonkers J, Wessels L. Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic acids research 2008, 36(2). 2241875, 18187509.
    • (2008) Nucleic acids research , vol.36 , Issue.2
    • Klijn, C.1    Holstege, H.2    de Ridder, J.3    Liu, X.4    Reinders, M.5    Jonkers, J.6    Wessels, L.7
  • 38
    • 62549085618 scopus 로고    scopus 로고
    • Human genetic variation and its contribution to complex traits
    • Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nat Rev Genet 2009, 10(4):241-251.
    • (2009) Nat Rev Genet , vol.10 , Issue.4 , pp. 241-251
    • Frazer, K.A.1    Murray, S.S.2    Schork, N.J.3    Topol, E.J.4
  • 40
    • 34347344982 scopus 로고    scopus 로고
    • Major changes in our DNA lead to major changes in our thinking
    • Sebat J. Major changes in our DNA lead to major changes in our thinking. Nature Genetics 2007, 39:S3-S5.
    • (2007) Nature Genetics , vol.39
    • Sebat, J.1
  • 42
    • 0024610919 scopus 로고
    • A tutorial on hidden Markov models and selected applications in speech recognition
    • Rabiner LR. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 1990, 77:257-286.
    • (1990) Proceedings of the IEEE , vol.77 , pp. 257-286
    • Rabiner, L.R.1
  • 43
    • 0036489069 scopus 로고    scopus 로고
    • Bayesian methods for hidden Markov models: Recursive computing in the 21st century
    • Scott S. Bayesian methods for hidden Markov models: Recursive computing in the 21st century. JASA 2002, 97:337-351.
    • (2002) JASA , vol.97 , pp. 337-351
    • Scott, S.1
  • 44
    • 33645791324 scopus 로고    scopus 로고
    • What HMMs can do
    • Bilmes J. What HMMs can do. IEICE Trans Inf & Syst 2006, E89-D(3):869-891.
    • (2006) IEICE Trans Inf & Syst , vol.E89-D , Issue.3 , pp. 869-891
    • Bilmes, J.1
  • 46
    • 1842475973 scopus 로고    scopus 로고
    • High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization
    • Nakao K, Mehta K, Fridlyand J, Moore D, Jain A, Lafuente A, Wiencke J, Terdiman J, Waldman F. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis 2004, 25(8):1345-1357.
    • (2004) Carcinogenesis , vol.25 , Issue.8 , pp. 1345-1357
    • Nakao, K.1    Mehta, K.2    Fridlyand, J.3    Moore, D.4    Jain, A.5    Lafuente, A.6    Wiencke, J.7    Terdiman, J.8    Waldman, F.9
  • 47
    • 3142691130 scopus 로고    scopus 로고
    • Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas
    • Douglas E, Fiegler H, Rowan A, Halford S, Bicknell D, Bodmer W, Tomlinson I, Carter N. Array comparative genomic hybridization analysis of colorectal cancer cell lines and primary carcinomas. Cancer Res 2004, 64(14):4817-4825.
    • (2004) Cancer Res , vol.64 , Issue.14 , pp. 4817-4825
    • Douglas, E.1    Fiegler, H.2    Rowan, A.3    Halford, S.4    Bicknell, D.5    Bodmer, W.6    Tomlinson, I.7    Carter, N.8
  • 48
    • 0032542364 scopus 로고    scopus 로고
    • Genetic instabilities in human cancers
    • Lengauer C, Kinzler K, Vogelstein B. Genetic instabilities in human cancers. Nature 1998, 396:643-649.
    • (1998) Nature , vol.396 , pp. 643-649
    • Lengauer, C.1    Kinzler, K.2    Vogelstein, B.3
  • 49
    • 34250615012 scopus 로고    scopus 로고
    • CGHregions: Dimension reduction for array CGh data with minimal information loss
    • Wiel MA, van Wieringen W. CGHregions: Dimension reduction for array CGh data with minimal information loss. Cancer Informatics 2007, 2:55-63.
    • (2007) Cancer Informatics , vol.2 , pp. 55-63
    • Wiel, M.A.1    van Wieringen, W.2
  • 50
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572.
    • (2004) Biostatistics , vol.5 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 51
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B 1995, 57:289-300.
    • (1995) J Roy Statist Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 58
    • 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
    • 2045149, 17921354
    • Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research 2007, 17(11):1665-1674. 2045149, 17921354.
    • (2007) Genome Research , vol.17 , Issue.11 , pp. 1665-1674
    • Wang, K.1    Li, M.2    Hadley, D.3    Liu, R.4    Glessner, J.5    Grant, S.F.A.6    Hakonarson, H.7    Bucan, M.8
  • 60
    • 67650556405 scopus 로고    scopus 로고
    • Accounting for uncertainty when assessing association between copy number and disease: a latent class model
    • 2707368, 19500389
    • Gonzalez J, Subirana I, Escaramis G, Peraza S, Caceres A, Estivill X, Armengol L. Accounting for uncertainty when assessing association between copy number and disease: a latent class model. BMC Bioinformatics 2009, 10:172+. 2707368, 19500389.
    • (2009) BMC Bioinformatics , vol.10
    • Gonzalez, J.1    Subirana, I.2    Escaramis, G.3    Peraza, S.4    Caceres, A.5    Estivill, X.6    Armengol, L.7
  • 61
    • 42249103276 scopus 로고    scopus 로고
    • On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test
    • Ionita-Laza I, Perry GH, Raby BA, Klanderman B, Lee C, Laird NM, Weiss ST, Lange C. On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test. Genetic epidemiology 2008, 32(3):273-284.
    • (2008) Genetic epidemiology , vol.32 , Issue.3 , pp. 273-284
    • Ionita-Laza, I.1    Perry, G.H.2    Raby, B.A.3    Klanderman, B.4    Lee, C.5    Laird, N.M.6    Weiss, S.T.7    Lange, C.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.