메뉴 건너뛰기




Volumn 19, Issue 40, 2013, Pages 6784-6793

Clinical applications of next-generation sequencing in colorectal cancers

Author keywords

Cancer genomics; Colorectal cancers; Next generation sequencing; Personalized medicine; The cancer genome atlas

Indexed keywords

APC PROTEIN; B RAF KINASE; K RAS PROTEIN; PROTEIN P53; SMAD4 PROTEIN; T CELL FACTOR PROTEIN; TRANSFORMING GROWTH FACTOR BETA;

EID: 84886999166     PISSN: 10079327     EISSN: 22192840     Source Type: Journal    
DOI: 10.3748/wjg.v19.i40.6784     Document Type: Review
Times cited : (31)

References (89)
  • 1
    • 0025280477 scopus 로고
    • Primary prevention of colorectal cancer. The WHO Collaborating Centre for the Prevention of Colorectal Cancer
    • [PMID: 2203551]
    • Shike M, Winawer SJ, Greenwald PH, Bloch A, Hill MJ, Swaroop SV. Primary prevention of colorectal cancer. The WHO Collaborating Centre for the Prevention of Colorectal Cancer. Bull World Health Organ 1990; 68: 377-385 [PMID: 2203551]
    • (1990) Bull World Health Organ , vol.68 , pp. 377-385
    • Shike, M.1    Winawer, S.J.2    Greenwald, P.H.3    Bloch, A.4    Hill, M.J.5    Swaroop, S.V.6
  • 3
    • 6944230093 scopus 로고    scopus 로고
    • Colon cancer survival rates with the new American Joint Committee on Cancer sixth edition staging
    • [PMID: 15467030]
    • O'Connell JB, Maggard MA, Ko CY. Colon cancer survival rates with the new American Joint Committee on Cancer sixth edition staging. J Natl Cancer Inst 2004; 96: 1420-1425 [PMID: 15467030]
    • (2004) J Natl Cancer Inst , vol.96 , pp. 1420-1425
    • O'Connell, J.B.1    Maggard, M.A.2    Ko, C.Y.3
  • 4
    • 79751489596 scopus 로고    scopus 로고
    • Molecular genetics of colorectal cancer
    • [PMID: 21090969 DOI: 10.1146/ annurev-pathol-011110-130235]
    • Fearon ER. Molecular genetics of colorectal cancer. Annu Rev Pathol 2011; 6: 479-507 [PMID: 21090969 DOI: 10.1146/ annurev-pathol-011110-130235]
    • (2011) Annu Rev Pathol , vol.6 , pp. 479-507
    • Fearon, E.R.1
  • 5
    • 66149133290 scopus 로고    scopus 로고
    • The impact of dietary and lifestyle risk factors on risk of colorectal cancer: A quantitative overview of the epidemiological evidence
    • [PMID: 19350627 DOI: 10.1002/ijc.24343]
    • Huxley RR, Ansary-Moghaddam A, Clifton P, Czernichow S, Parr CL, Woodward M. The impact of dietary and lifestyle risk factors on risk of colorectal cancer: a quantitative overview of the epidemiological evidence. Int J Cancer 2009; 125: 171-180 [PMID: 19350627 DOI: 10.1002/ijc.24343]
    • (2009) Int J Cancer , vol.125 , pp. 171-180
    • Huxley, R.R.1    Ansary-Moghaddam, A.2    Clifton, P.3    Czernichow, S.4    Parr, C.L.5    Woodward, M.6
  • 6
    • 33845649043 scopus 로고    scopus 로고
    • Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridization
    • [PMID: 17087931 DOI: 10.1053/ j.gastro.2006.10.021]
    • Kim MY, Yim SH, Kwon MS, Kim TM, Shin SH, Kang HM, Lee C, Chung YJ. Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridization. Gastroenterology 2006; 131: 1913-1924 [PMID: 17087931 DOI: 10.1053/ j.gastro.2006.10.021]
    • (2006) Gastroenterology , vol.131 , pp. 1913-1924
    • Kim, M.Y.1    Yim, S.H.2    Kwon, M.S.3    Kim, T.M.4    Shin, S.H.5    Kang, H.M.6    Lee, C.7    Chung, Y.J.8
  • 7
    • 0034303643 scopus 로고    scopus 로고
    • Molecular profiling of human cancer
    • [PMID: 11262874 DOI: 10.1038/35049567]
    • Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000; 1: 48-56 [PMID: 11262874 DOI: 10.1038/35049567]
    • (2000) Nat Rev Genet , vol.1 , pp. 48-56
    • Liotta, L.1    Petricoin, E.2
  • 8
    • 64749094310 scopus 로고    scopus 로고
    • The cancer genome
    • [PMID: 19360079 DOI: 10.1038/nature07943]
    • Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature 2009; 458: 719-724 [PMID: 19360079 DOI: 10.1038/nature07943]
    • (2009) Nature , vol.458 , pp. 719-724
    • Stratton, M.R.1    Campbell, P.J.2    Futreal, P.A.3
  • 9
    • 53649101617 scopus 로고    scopus 로고
    • What would you do if you could sequence everything?
    • [PMID: 18846086 DOI: 10.1038/nbt1494]
    • Kahvejian A, Quackenbush J, Thompson JF. What would you do if you could sequence everything? Nat Biotechnol 2008; 26: 1125-1133 [PMID: 18846086 DOI: 10.1038/nbt1494]
    • (2008) Nat Biotechnol , vol.26 , pp. 1125-1133
    • Kahvejian, A.1    Quackenbush, J.2    Thompson, J.F.3
  • 10
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • [PMID: 18846087 DOI: 10.1038/ nbt1486]
    • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26: 1135-1145 [PMID: 18846087 DOI: 10.1038/ nbt1486]
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 12
    • 84862496309 scopus 로고    scopus 로고
    • Genome sequencing and cancer
    • [PMID: 22534183 DOI: 10.1016/ j.gde.2012.03.005]
    • Mardis ER. Genome sequencing and cancer. Curr Opin Genet Dev 2012; 22: 245-250 [PMID: 22534183 DOI: 10.1016/ j.gde.2012.03.005]
    • (2012) Curr Opin Genet Dev , vol.22 , pp. 245-250
    • Mardis, E.R.1
  • 13
    • 77956838065 scopus 로고    scopus 로고
    • Advances in understanding cancer genomes through second-generation sequencing
    • [PMID: 20847746 DOI: 10.1038/ nrg2841]
    • Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010; 11: 685-696 [PMID: 20847746 DOI: 10.1038/ nrg2841]
    • (2010) Nat Rev Genet , vol.11 , pp. 685-696
    • Meyerson, M.1    Gabriel, S.2    Getz, G.3
  • 19
    • 72449176846 scopus 로고    scopus 로고
    • Molecular origins of cancer: Molecular basis of colorectal cancer
    • [PMID: 20018966 DOI: 10.1056/NEJMra0804588]
    • Markowitz SD, Bertagnolli MM. Molecular origins of cancer: Molecular basis of colorectal cancer. N Engl J Med 2009; 361: 2449-2460 [PMID: 20018966 DOI: 10.1056/NEJMra0804588]
    • (2009) N Engl J Med , vol.361 , pp. 2449-2460
    • Markowitz, S.D.1    Bertagnolli, M.M.2
  • 22
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • Cancer Genome Atlas Network. [PMID: 22810696 DOI: 10.1038/nature11252]
    • Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330-337 [PMID: 22810696 DOI: 10.1038/nature11252]
    • (2012) Nature , vol.487 , pp. 330-337
  • 23
    • 54549108740 scopus 로고    scopus 로고
    • Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • [PMID: 18772890 DOI: 10.1038/nature07385]
    • Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455: 1061-1068 [PMID: 18772890 DOI: 10.1038/nature07385]
    • (2008) Nature , vol.455 , pp. 1061-1068
  • 24
    • 59149089747 scopus 로고    scopus 로고
    • Sox9 inhibits Wnt signaling by promoting beta-catenin phosphorylation in the nucleus
    • [PMID: 19047045 DOI: 10.1074/jbc.M808048200]
    • Topol L, Chen W, Song H, Day TF, Yang Y. Sox9 inhibits Wnt signaling by promoting beta-catenin phosphorylation in the nucleus. J Biol Chem 2009; 284: 3323-3333 [PMID: 19047045 DOI: 10.1074/jbc.M808048200]
    • (2009) J Biol Chem , vol.284 , pp. 3323-3333
    • Topol, L.1    Chen, W.2    Song, H.3    Day, T.F.4    Yang, Y.5
  • 26
    • 69749086899 scopus 로고    scopus 로고
    • Identification of rare cancer driver mutations by network reconstruction
    • [PMID: 19574499 DOI: 10.1101/gr.092833.109]
    • Torkamani A, Schork NJ. Identification of rare cancer driver mutations by network reconstruction. Genome Res 2009; 19: 1570-1578 [PMID: 19574499 DOI: 10.1101/gr.092833.109]
    • (2009) Genome Res , vol.19 , pp. 1570-1578
    • Torkamani, A.1    Schork, N.J.2
  • 29
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • [PMID: 16824020 DOI: 10.1146/annurev. genom.7.080505.115630]
    • Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006; 7: 61-80 [PMID: 16824020 DOI: 10.1146/annurev. genom.7.080505.115630]
    • (2006) Annu Rev Genomics Hum Genet , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 35
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • [PMID: 14735121 DOI: 10.1038/nrg1272]
    • Barabási AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004; 5: 101-113 [PMID: 14735121 DOI: 10.1038/nrg1272]
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.L.1    Oltvai, Z.N.2
  • 36
    • 16844376909 scopus 로고    scopus 로고
    • Reverse engineering of regulatory networks in human B cells
    • [PMID: 15778709 DOI: 10.1038/ng1532]
    • Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005; 37: 382-390 [PMID: 15778709 DOI: 10.1038/ng1532]
    • (2005) Nat Genet , vol.37 , pp. 382-390
    • Basso, K.1    Margolin, A.A.2    Stolovitzky, G.3    Klein, U.4    Dalla-Favera, R.5    Califano, A.6
  • 37
    • 5044245707 scopus 로고    scopus 로고
    • Gene coexpression network topology provides a framework for molecular characterization of cellular state
    • [PMID: 15130938 DOI: 10.1093/bioinformatics/ bth234]
    • Carter SL, Brechbühler CM, Griffin M, Bond AT. Gene coexpression network topology provides a framework for molecular characterization of cellular state. Bioinformatics 2004; 20: 2242-2250 [PMID: 15130938 DOI: 10.1093/bioinformatics/ bth234]
    • (2004) Bioinformatics , vol.20 , pp. 2242-2250
    • Carter, S.L.1    Brechbühler, C.M.2    Griffin, M.3    Bond, A.T.4
  • 38
    • 79959838081 scopus 로고    scopus 로고
    • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma
    • [PMID: 21720365 DOI: 10.1038/nature10166]
    • Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-615 [PMID: 21720365 DOI: 10.1038/nature10166]
    • (2011) Nature , vol.474 , pp. 609-615
  • 39
    • 84856535081 scopus 로고    scopus 로고
    • Mutual exclusivity analysis identifies oncogenic network modules
    • [PMID: 21908773 DOI: 10.1101/ gr.125567.111]
    • Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res 2012; 22: 398-406 [PMID: 21908773 DOI: 10.1101/ gr.125567.111]
    • (2012) Genome Res , vol.22 , pp. 398-406
    • Ciriello, G.1    Cerami, E.2    Sander, C.3    Schultz, N.4
  • 47
    • 35648929376 scopus 로고    scopus 로고
    • Mining microsatellites in eukaryotic genomes
    • [PMID: 17945369 DOI: 10.1016/j.tibtech.2007.07.013]
    • Sharma PC, Grover A, Kahl G. Mining microsatellites in eukaryotic genomes. Trends Biotechnol 2007; 25: 490-498 [PMID: 17945369 DOI: 10.1016/j.tibtech.2007.07.013]
    • (2007) Trends Biotechnol , vol.25 , pp. 490-498
    • Sharma, P.C.1    Grover, A.2    Kahl, G.3
  • 48
    • 77449130761 scopus 로고    scopus 로고
    • Microsatellite instability in colorectal cancer
    • [PMID: 20420947 DOI: 10.1053/j.gastro.2009.12.064] 2073-2087.e3
    • Boland CR, Goel A. Microsatellite instability in colorectal cancer. Gastroenterology 2010; 138: 2073-2087. e3 [PMID: 20420947 DOI: 10.1053/j.gastro.2009.12.064]
    • (2010) Gastroenterology , vol.138
    • Boland, C.R.1    Goel, A.2
  • 49
    • 0028221943 scopus 로고
    • Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer
    • [PMID: 8145827 DOI: 10.1038/368258a0]
    • Bronner CE, Baker SM, Morrison PT, Warren G, Smith LG, Lescoe MK, Kane M, Earabino C, Lipford J, Lindblom A. Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature 1994; 368: 258-261 [PMID: 8145827 DOI: 10.1038/368258a0]
    • (1994) Nature , vol.368 , pp. 258-261
    • Bronner, C.E.1    Baker, S.M.2    Morrison, P.T.3    Warren, G.4    Smith, L.G.5    Lescoe, M.K.6    Kane, M.7    Earabino, C.8    Lipford, J.9    Lindblom, A.10
  • 54
    • 0345357773 scopus 로고    scopus 로고
    • Gene silencing in cancer in association with promoter hypermethylation
    • [PMID: 14627790 DOI: 10.1056/NEJMra023075]
    • Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003; 349: 2042-2054 [PMID: 14627790 DOI: 10.1056/NEJMra023075]
    • (2003) N Engl J Med , vol.349 , pp. 2042-2054
    • Herman, J.G.1    Baylin, S.B.2
  • 55
    • 0036274359 scopus 로고    scopus 로고
    • The fundamental role of epigenetic events in cancer
    • [PMID: 12042769]
    • Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002; 3: 415-428 [PMID: 12042769]
    • (2002) Nat Rev Genet , vol.3 , pp. 415-428
    • Jones, P.A.1    Baylin, S.B.2
  • 56
  • 57
    • 33646369393 scopus 로고    scopus 로고
    • Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
    • [PMID: 16642018 DOI: 10.1038/ng1781]
    • Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark SJ. Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nat Genet 2006; 38: 540-549 [PMID: 16642018 DOI: 10.1038/ng1781]
    • (2006) Nat Genet , vol.38 , pp. 540-549
    • Frigola, J.1    Song, J.2    Stirzaker, C.3    Hinshelwood, R.A.4    Peinado, M.A.5    Clark, S.J.6
  • 63
    • 39749113080 scopus 로고    scopus 로고
    • Clonal integration of a polyomavirus in human Merkel cell carcinoma
    • [PMID: 18202256 DOI: 10.1126/science. 1152586]
    • Feng H, Shuda M, Chang Y, Moore PS. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 2008; 319: 1096-1100 [PMID: 18202256 DOI: 10.1126/science. 1152586]
    • (2008) Science , vol.319 , pp. 1096-1100
    • Feng, H.1    Shuda, M.2    Chang, Y.3    Moore, P.S.4
  • 64
    • 0036479008 scopus 로고    scopus 로고
    • Identification of foreign gene sequences by transcript filtering against the human genome
    • [PMID: 11788827]
    • Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet 2002; 30: 141-142 [PMID: 11788827]
    • (2002) Nat Genet , vol.30 , pp. 141-142
    • Weber, G.1    Shendure, J.2    Tanenbaum, D.M.3    Church, G.M.4    Meyerson, M.5
  • 65
    • 79955778143 scopus 로고    scopus 로고
    • PathSeq: Software to identify or discover microbes by deep sequencing of human tissue
    • [PMID: 21552235 DOI: 10.1038/ nbt.1868]
    • Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M. PathSeq: software to identify or discover microbes by deep sequencing of human tissue. Nat Biotechnol 2011; 29: 393-396 [PMID: 21552235 DOI: 10.1038/ nbt.1868]
    • (2011) Nat Biotechnol , vol.29 , pp. 393-396
    • Kostic, A.D.1    Ojesina, A.I.2    Pedamallu, C.S.3    Jung, J.4    Verhaak, R.G.5    Getz, G.6    Meyerson, M.7
  • 70
    • 84869065150 scopus 로고    scopus 로고
    • Chromothripsis: Chromosomes in crisis
    • [PMID: 23153487 DOI: 10.1016/j.devcel.2012.10.010]
    • Jones MJ, Jallepalli PV. Chromothripsis: chromosomes in crisis. Dev Cell 2012; 23: 908-917 [PMID: 23153487 DOI: 10.1016/j.devcel.2012.10.010]
    • (2012) Dev Cell , vol.23 , pp. 908-917
    • Jones, M.J.1    Jallepalli, P.V.2
  • 72
    • 84873391241 scopus 로고    scopus 로고
    • Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes
    • [PMID: 23132910 DOI: 10.1101/gr.140301.112]
    • Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res 2013; 23: 217-227 [PMID: 23132910 DOI: 10.1101/gr.140301.112]
    • (2013) Genome Res , vol.23 , pp. 217-227
    • Kim, T.M.1    Xi, R.2    Luquette, L.J.3    Park, R.W.4    Johnson, M.D.5    Park, P.J.6
  • 80
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • [PMID: 19736561 DOI: 10.1038/nrg2641]
    • Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009; 10: 669-680 [PMID: 19736561 DOI: 10.1038/nrg2641]
    • (2009) Nat Rev Genet , vol.10 , pp. 669-680
    • Park, P.J.1
  • 85
    • 84871726922 scopus 로고    scopus 로고
    • Exome capture sequencing of adenoma reveals genetic alterations in multiple cellular pathways at the early stage of colorectal tumorigenesis
    • [PMID: 23301059 DOI: 10.1371/journal.pone.0053310]
    • Zhou D, Yang L, Zheng L, Ge W, Li D, Zhang Y, Hu X, Gao Z, Xu J, Huang Y, Hu H, Zhang H, Zhang H, Liu M, Yang H, Zheng L, Zheng S. Exome capture sequencing of adenoma reveals genetic alterations in multiple cellular pathways at the early stage of colorectal tumorigenesis. PLoS One 2013; 8: e53310 [PMID: 23301059 DOI: 10.1371/journal.pone.0053310]
    • (2013) PLoS One , vol.8
    • Zhou, D.1    Yang, L.2    Zheng, L.3    Ge, W.4    Li, D.5    Zhang, Y.6    Hu, X.7    Gao, Z.8    Xu, J.9    Huang, Y.10    Hu, H.11    Zhang, H.12    Zhang, H.13    Liu, M.14    Yang, H.15    Zheng, L.16    Zheng, S.17
  • 87
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • [PMID: 19451168 DOI: 10.1093/bioinformatics/ btp324]
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-1760 [PMID: 19451168 DOI: 10.1093/bioinformatics/ btp324]
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 89
    • 84874678421 scopus 로고    scopus 로고
    • Mutation spectrum in human colorectal cancers and potential functional relevance
    • [PMID: 23497483]
    • Yin H, Liang Y, Yan Z, Liu B, Su Q. Mutation spectrum in human colorectal cancers and potential functional relevance. BMC Med Genet 2013; 14: 32 [PMID: 23497483]
    • (2013) BMC Med Genet , vol.14 , pp. 32
    • Yin, H.1    Liang, Y.2    Yan, Z.3    Liu, B.4    Su, Q.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.