메뉴 건너뛰기




Volumn 3, Issue , 2012, Pages

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE;

EID: 84866067741     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms1982     Document Type: Article
Times cited : (103)

References (42)
  • 1
    • 79960036578 scopus 로고    scopus 로고
    • Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
    • Puente, X. S. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-105 (2011).
    • (2011) Nature , vol.475 , pp. 101-105
    • Puente, X.S.1
  • 2
    • 74449085934 scopus 로고    scopus 로고
    • A small-cell lung cancer genome with complex signatures of tobacco exposure
    • Pleasance, E. D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184-190 (2010).
    • (2010) Nature , vol.463 , pp. 184-190
    • Pleasance, E.D.1
  • 3
    • 74449093973 scopus 로고    scopus 로고
    • A comprehensive catalogue of somatic mutations from a human cancer genome
    • Pleasance, E. D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191-196 (2010).
    • (2010) Nature , vol.463 , pp. 191-196
    • Pleasance, E.D.1
  • 4
    • 77953006634 scopus 로고    scopus 로고
    • The mutation spectrum revealed by paired genome sequences from a lung cancer patient
    • Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473-477 (2010).
    • (2010) Nature , vol.465 , pp. 473-477
    • Lee, W.1
  • 5
    • 79951497419 scopus 로고    scopus 로고
    • The genomic complexity of primary human prostate cancer
    • Berger, M. F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214-220 (2011).
    • (2011) Nature , vol.470 , pp. 214-220
    • Berger, M.F.1
  • 6
    • 80053385552 scopus 로고    scopus 로고
    • Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    • Bass, A. J. et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat. Genet. 43, 964-968 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 964-968
    • Bass, A.J.1
  • 7
    • 79959838081 scopus 로고    scopus 로고
    • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma
    • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609-615 (2011).
    • (2011) Nature , vol.474 , pp. 609-615
  • 8
    • 79951494668 scopus 로고    scopus 로고
    • Initial genome sequencing and analysis of multiple myeloma
    • Chapman, M. A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467-472 (2011).
    • (2011) Nature , vol.471 , pp. 467-472
    • Chapman, M.A.1
  • 9
    • 80052158097 scopus 로고    scopus 로고
    • The Mutational landscape of head and neck squamous cell carcinoma
    • Stransky, N. et al. The Mutational landscape of head and neck squamous cell carcinoma. Science (2011).
    • (2011) Science
    • Stransky, N.1
  • 10
    • 82255183148 scopus 로고    scopus 로고
    • Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer
    • Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet. 43, 1219-1223 (2011).
    • (2011) Nat. Genet , vol.43 , pp. 1219-1223
    • Wang, K.1
  • 11
    • 77951115122 scopus 로고    scopus 로고
    • International Cancer Genome Consortium International network of cancer genome projects
    • International Cancer Genome Consortium et al. International network of cancer genome projects. Nature 464, 993-998 (2010).
    • (2010) Nature , vol.464 , pp. 993-998
  • 12
    • 0017167185 scopus 로고
    • The clonal evolution of tumor cell populations
    • Nowell, P. C. The clonal evolution of tumor cell populations. Science 194, 23-28 (1976).
    • (1976) Science , vol.194 , pp. 23-28
    • Nowell, P.C.1
  • 13
    • 84983720414 scopus 로고    scopus 로고
    • Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data
    • Tao, Y. et al. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc. Natl Acad. Sci. USA 108, 12042-12047 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 12042-12047
    • Tao, Y.1
  • 14
    • 1542619851 scopus 로고    scopus 로고
    • Dynamics of cancer progression
    • Michor, F., Iwasa, Y.&;'Nowak, M. A. Dynamics of cancer progression. Nat. Rev. Cancer. 4, 197-205 (2004). (Pubitemid 38337499)
    • (2004) Nature Reviews Cancer , vol.4 , Issue.3 , pp. 197-205
    • Michor, F.1    Iwasa, Y.2    Nowak, M.A.3
  • 15
    • 33845243362 scopus 로고    scopus 로고
    • Cancer as an evolutionary and ecological process
    • DOI 10.1038/nrc2013, PII NRC2013
    • Merlo, L. M., Pepper, J. W., Reid, B. J.&;'Maley, C. C. Cancer as an evolutionary and ecological process. Nat. Rev. Cancer. 6, 924-935 (2006). (Pubitemid 44862677)
    • (2006) Nature Reviews Cancer , vol.6 , Issue.12 , pp. 924-935
    • Merlo, L.M.F.1    Pepper, J.W.2    Reid, B.J.3    Maley, C.C.4
  • 16
    • 75749103383 scopus 로고    scopus 로고
    • Molecular spectrum, and consequences of human mutation
    • Lynch, M. Rate, molecular spectrum, and consequences of human mutation. Proc. Natl Acad. Sci. USA 107, 961-968 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 961-968
    • Lynch, M.1
  • 17
    • 83255165727 scopus 로고    scopus 로고
    • High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
    • Fudenberg, G., Getz, G., Meyerson, M.&;'Mirny, L. A. High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol. 19, 1109-1113 (2011).
    • (2011) Nat. Biotechnol , vol.19 , pp. 1109-1113
    • Fudenberg, G.1    Getz, G.2    Meyerson, M.3    Mirny, L.A.4
  • 18
    • 83255189766 scopus 로고    scopus 로고
    • DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes
    • De, S.&;'Michor, F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol. 29, 1103-1108 (2011).
    • (2011) Nat. Biotechnol , vol.29 , pp. 1103-1108
    • De, S.1    Michor, F.2
  • 20
    • 52949127312 scopus 로고    scopus 로고
    • An integrated genomic analysis of human glioblastoma multiforme
    • Parsons, D. W. et al. An integrated genomic analysis of human glioblastoma multiforme. Science 321, 1807-1812 (2008).
    • (2008) Science , vol.321 , pp. 1807-1812
    • Parsons, D.W.1
  • 21
    • 84866118244 scopus 로고    scopus 로고
    • The large-scale distribution of somatic mutations in cancer genomes
    • Hodgkinson, A., Chen, Y.&;'Eyre-Walker, A. The large-scale distribution of somatic mutations in cancer genomes. Hum. Mutat. (2011).
    • (2011) Hum. Mutat
    • Hodgkinson, A.1    Chen, Y.2    Eyre-Walker, A.3
  • 22
    • 63449141981 scopus 로고    scopus 로고
    • Human mutation rate associated with DNA replication timing
    • Stamatoyannopoulos, J. A. et al. Human mutation rate associated with DNA replication timing. Nat. Genet. 41, 393-395 (2009).
    • (2009) Nat. Genet , vol.41 , pp. 393-395
    • Stamatoyannopoulos, J.A.1
  • 23
    • 77950661675 scopus 로고    scopus 로고
    • Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
    • Chen, C. L. et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res. 20, 447-457 (2010).
    • (2010) Genome Res , vol.20 , pp. 447-457
    • Chen, C.L.1
  • 24
    • 76349123622 scopus 로고    scopus 로고
    • Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
    • Hansen, R. S. et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc. Natl Acad. Sci. USA 107, 139-144 (2010).
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 139-144
    • Hansen, R.S.1
  • 25
    • 0036640951 scopus 로고    scopus 로고
    • Human SNP variability and mutation rate are higher in regions of high recombination
    • DOI 10.1016/S0168-9525(02)02669-0, PII S0168952502026690
    • Lercher, M. J.&;'Hurst, L. D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18, 337-340 (2002). (Pubitemid 34804439)
    • (2002) Trends in Genetics , vol.18 , Issue.7 , pp. 337-340
    • Lercher, M.J.1    Hurst, L.D.2
  • 26
    • 0024966756 scopus 로고
    • Chromosomal location and evolutionary rate variation in enterobacterial genes
    • Sharp, P. M., Shields, D. C., Wolfe, K. H.&;'Li, W. H. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246, 808-810 (1989).
    • (1989) Science , vol.246 , pp. 808-810
    • Sharp, P.M.1    Shields, D.C.2    Wolfe, K.H.3    Li, W.H.4
  • 27
    • 80055024376 scopus 로고    scopus 로고
    • Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
    • Lin, M. F. et al. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res. 21, 1916-1928 (2011).
    • (2011) Genome Res , vol.21 , pp. 1916-1928
    • Lin, M.F.1
  • 28
    • 80052964856 scopus 로고    scopus 로고
    • Understanding the contribution of synonymous mutations to human disease
    • Sauna, Z. E.&;'Kimchi-Sarfaty, C. Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet. 12, 683-691 (2011).
    • (2011) Nat. Rev. Genet , vol.12 , pp. 683-691
    • Sauna, Z.E.1    Kimchi-Sarfaty, C.2
  • 29
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • DOI 10.1101/gr.176601
    • Ng, P. C.&;'Henikoff, S. Predicting deleterious amino acid substitutions. Genome Res. 11, 863-874 (2001). (Pubitemid 32447869)
    • (2001) Genome Research , vol.11 , Issue.5 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 33
    • 0034025692 scopus 로고    scopus 로고
    • Adaptation and the cost of complexity
    • Orr, H. A. Adaptation and the cost of complexity. Evolution 54, 13-20 (2000). (Pubitemid 30186263)
    • (2000) Evolution , vol.54 , Issue.1 , pp. 13-20
    • Orr, H.A.1
  • 34
    • 77952994784 scopus 로고    scopus 로고
    • Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
    • Ryba, T. et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761-770 (2010).
    • (2010) Genome Res , vol.20 , pp. 761-770
    • Ryba, T.1
  • 35
    • 77957369058 scopus 로고    scopus 로고
    • Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture
    • Yaffe, E. et al. Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet. 6, e1001011 (2010).
    • (2010) PLoS Genet , vol.6
    • Yaffe, E.1
  • 38
    • 84975742565 scopus 로고    scopus 로고
    • 1000 Genomes Project Consortium.. A map of human genome variation from population-scale sequencing
    • 1000 Genomes Project Consortium.. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 39
    • 67650064594 scopus 로고    scopus 로고
    • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    • Pruitt, K. D. et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 19, 1316-1323 (2009).
    • (2009) Genome Res , vol.19 , pp. 1316-1323
    • Pruitt, K.D.1
  • 40
    • 33748645500 scopus 로고    scopus 로고
    • GENCODE: Producing a reference annotation for ENCODE
    • Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7 (Suppl 1), S4.1-S4.9 (2006).
    • (2006) Genome Biol , vol.7 , Issue.SUPPL. 1
    • Harrow, J.1
  • 42
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A.&;'Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
    • (2010) Genome Biol , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.