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Volumn 2, Issue 2, 2010, Pages 199-207

Next-generation sequencing technologies for DNA methylation analyses in cancer genomics

Author keywords

cancer; genome wide; methylome; next generation sequencing technology

Indexed keywords

DNA;

EID: 77954101917     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.09.50     Document Type: Review
Times cited : (12)

References (41)
  • 1
    • 0034682403 scopus 로고    scopus 로고
    • The DNA sequence of human chromosome 21
    • Hattori M, Fujiyama A, Taylor TD et al.: The DNA sequence of human chromosome 21. Nature 405 (6784), 311-319 (2000).
    • (2000) Nature , vol.405 , Issue.6784 , pp. 311-319
    • Hattori, M.1    Fujiyama, A.2    Taylor, T.D.3
  • 2
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis ER: Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
    • (2008) Annu. Rev. Genomics Hum. Genet , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 3
    • 33847293670 scopus 로고    scopus 로고
    • High-throughput oncogene mutation profling in human cancer
    • Thomas RK, Baker AC, Debiasi RM et al.: High-throughput oncogene mutation profling in human cancer. Nat. Genet. 39(3), 347-351 (2007).
    • (2007) Nat. Genet , vol.39 , Issue.3 , pp. 347-351
    • Thomas, R.K.1    Baker, A.C.2    Debiasi, R.M.3
  • 4
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057), 376-380 (2005).
    • (2005) Nature , vol.437 , Issue.7057 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 5
    • 45549096818 scopus 로고    scopus 로고
    • Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
    • Bock C, Walter J, Paulsen M, Lengauer T: Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res. 36(10), E55 (2008).
    • (2008) Nucleic Acids Res , vol.36 , Issue.10
    • Bock, C.1    Walter, J.2    Paulsen, M.3    Lengauer, T.4
  • 6
    • 34249275353 scopus 로고    scopus 로고
    • Phenotypic plasticity and the epigenetics of human disease
    • Feinberg AP: Phenotypic plasticity and the epigenetics of human disease. Nature 447(7143), 433-440 (2007).
    • (2007) Nature , vol.447 , Issue.7143 , pp. 433-440
    • Feinberg, A.P.1
  • 7
    • 70549086900 scopus 로고    scopus 로고
    • Epigenetic mechanisms in cancer
    • Banerjee HN, Verma M: Epigenetic mechanisms in cancer. Biomark. Med. 3(4), 397-410 (2009).
    • (2009) Biomark. Med , vol.3 , Issue.4 , pp. 397-410
    • Banerjee, H.N.1    Verma, M.2
  • 8
    • 42649089780 scopus 로고    scopus 로고
    • The methylome: Approaches for global DNA methylation profling
    • Beck S, Rakyan VK: The methylome: approaches for global DNA methylation profling. Trends Genet. 24(5), 231-237 (2008).
    • (2008) Trends Genet , vol.24 , Issue.5 , pp. 231-237
    • Beck, S.1    Rakyan, V.K.2
  • 9
    • 59749105927 scopus 로고    scopus 로고
    • Genome-wide high throughput ana lysis of DNA methylation in eukaryotes
    • Pomraning KR, Smith KM, Freitag M: Genome-wide high throughput ana lysis of DNA methylation in eukaryotes. Methods 47(3), 142-150 (2009).
    • (2009) Methods , vol.47 , Issue.3 , pp. 142-150
    • Pomraning, K.R.1    Smith, K.M.2    Freitag, M.3
  • 10
    • 66449121652 scopus 로고    scopus 로고
    • Finding the ffth base: Genome-wide sequencing of cytosine methylation
    • Lister R, Ecker JR: Finding the ffth base: genome-wide sequencing of cytosine methylation. Genome Res. 19(6), 959-966 (2009).
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 959-966
    • Lister, R.1    Ecker, J.R.2
  • 11
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH et al.: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271), 315-322 (2009).
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3
  • 12
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specifc analyses identify sites of differential DNA methylation in normal and transformed human cells
    • Weber M, Davies JJ, Wittig D et al.: Chromosome-wide and promoter-specifc analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37(8), 853-862 (2005).
    • (2005) Nat. Genet , vol.37 , Issue.8 , pp. 853-862
    • Weber, M.1    Davies, J.J.2    Wittig, D.3
  • 13
    • 31744433660 scopus 로고    scopus 로고
    • Evidence for an instructive mechanism of de novo methylation in cancer cells
    • Keshet I, Schlesinger Y, Farkash S et al.: Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet. 38(2), 149-153 (2006).
    • (2006) Nat. Genet , vol.38 , Issue.2 , pp. 149-153
    • Keshet, I.1    Schlesinger, Y.2    Farkash, S.3
  • 14
    • 0028340280 scopus 로고
    • Purifcation of CpG islands using a methylated DNA binding column
    • Cross SH, Charlton JA, Nan X, Bird AP: Purifcation of CpG islands using a methylated DNA binding column. Nat. Genet. 6(3), 236-244 (1994).
    • (1994) Nat. Genet , vol.6 , Issue.3 , pp. 236-244
    • Cross, S.H.1    Charlton, J.A.2    Nan, X.3    Bird, A.P.4
  • 15
    • 50649108994 scopus 로고    scopus 로고
    • An integrated resource for genome-wide identifcation and ana lysis of human tissue-specifc differentially methylated regions (TDMRs)
    • Rakyan VK, Down TA, Thorne NP et al.: An integrated resource for genome-wide identifcation and ana lysis of human tissue-specifc differentially methylated regions (TDMRs). Genome Res. 18(9), 1518-1529 (2008).
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1518-1529
    • Rakyan, V.K.1    Down, T.A.2    Thorne, N.P.3
  • 16
    • 64349091471 scopus 로고    scopus 로고
    • Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    • Ball MP, Li JB, Gao Y et al.: Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27(4), 361-368 (2009).
    • (2009) Nat. Biotechnol , vol.27 , Issue.4 , pp. 361-368
    • Ball, M.P.1    Li, J.B.2    Gao, Y.3
  • 17
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber M, Hellmann I, Stadler MB et al.: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39(4), 457-466 (2007).
    • (2007) Nat. Genet , vol.39 , Issue.4 , pp. 457-466
    • Weber, M.1    Hellmann, I.2    Stadler, M.B.3
  • 18
    • 46949098742 scopus 로고    scopus 로고
    • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome ana lysis
    • Down TA, Rakyan VK, Turner DJ et al.: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome ana lysis. Nat. Biotechnol. 26(7), 779-785 (2008).
    • (2008) Nat. Biotechnol , vol.26 , Issue.7 , pp. 779-785
    • Down, T.A.1    Rakyan, V.K.2    Turner, D.J.3
  • 19
    • 33751505540 scopus 로고    scopus 로고
    • DNA methylation profling of human chromosomes 6, 20 and 22
    • Eckhardt F, Lewin J, Cortese R et al.: DNA methylation profling of human chromosomes 6, 20 and 22. Nat. Genet. 38(12), 1378-1385 (2006).
    • (2006) Nat. Genet. , vol.20 , Issue.22 , pp. 1378-1385
    • Eckhardt, F.1    Lewin, J.2    Cortese, R.3
  • 20
    • 33646369393 scopus 로고    scopus 로고
    • Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
    • 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. 38(5), 540-549 (2006).
    • (2006) Nat. Genet , vol.38 , Issue.5 , pp. 540-549
    • Frigola, J.1    Song, J.2    Stirzaker, C.3    Hinshelwood, R.A.4    Peinado, M.A.5    Clark, S.J.6
  • 21
    • 77449127799 scopus 로고    scopus 로고
    • MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
    • Serre D, Lee BH, Ting AH: MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 38(2), 391-399 (2009).
    • (2009) Nucleic Acids Res , vol.38 , Issue.2 , pp. 391-399
    • Serre, D.1    Lee, B.H.2    Ting, A.H.3
  • 22
    • 0026546877 scopus 로고
    • A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands
    • Frommer M, Mcdonald LE, Millar DS et al.: A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl Acad. Sci. USA 89(5), 1827-1831 (1992).
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , Issue.5 , pp. 1827-1831
    • Frommer, M.1    McDonald, L.E.2    Millar, D.S.3
  • 23
    • 0037068312 scopus 로고    scopus 로고
    • CpG island hypermethylation and tumor suppressor genes: A booming present, a brighter future
    • Esteller M: CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 21(35), 5427-5440 (2002).
    • (2002) Oncogene , vol.21 , Issue.35 , pp. 5427-5440
    • Esteller, M.1
  • 24
    • 65849333933 scopus 로고    scopus 로고
    • Preparation of genome-wide DNA fragment libraries using bisulfte in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection
    • Ranade SS, Chung CB, Zon G, Boyd VL: Preparation of genome-wide DNA fragment libraries using bisulfte in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection. Anal. Biochem. 390(2), 126-135 (2009).
    • (2009) Anal. Biochem , vol.390 , Issue.2 , pp. 126-135
    • Ranade, S.S.1    Chung, C.B.2    Zon, G.3    Boyd, V.L.4
  • 25
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfte sequence MAPping program
    • Xi Y, Li W: BSMAP: whole genome bisulfte sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 26
    • 40749109894 scopus 로고    scopus 로고
    • Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
    • Cokus SJ, Feng S, Zhang X et al.: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452(7184), 215-219 (2008).
    • (2008) Nature , vol.452 , Issue.7184 , pp. 215-219
    • Cokus, S.J.1    Feng, S.2    Zhang, X.3
  • 27
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • Lister R, O'Malley RC, Tonti-Filippini J et al.: Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3), 523-536 (2008).
    • (2008) Cell , vol.133 , Issue.3 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3
  • 28
    • 34548734299 scopus 로고    scopus 로고
    • Ultradeep bisulfte sequencing ana lysis of DNA methylation patterns in multiple gene promoters by 454 sequencing
    • Taylor KH, Kramer RS, Davis JW et al.: Ultradeep bisulfte sequencing ana lysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 67(18), 8511-8518 (2007).
    • (2007) Cancer Res , vol.67 , Issue.18 , pp. 8511-8518
    • Taylor, K.H.1    Kramer, R.S.2    Davis, J.W.3
  • 29
    • 38049073696 scopus 로고    scopus 로고
    • Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA
    • Korshunova Y, Maloney RK, Lakey N et al.: Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Res. 18(1), 19-29 (2008).
    • (2008) Genome Res , vol.18 , Issue.1 , pp. 19-29
    • Korshunova, Y.1    Maloney, R.K.2    Lakey, N.3
  • 30
    • 49649125042 scopus 로고    scopus 로고
    • Genome-scale DNA methylation maps of pluripotent and differentiated cells
    • Meissner A, Mikkelsen TS, Gu H et al.: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205), 766-770 (2008).
    • (2008) Nature , vol.454 , Issue.7205 , pp. 766-770
    • Meissner, A.1    Mikkelsen, T.S.2    Gu, H.3
  • 31
    • 65549107163 scopus 로고    scopus 로고
    • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    • Brunner AL, Johnson DS, Kim SW et al.: Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19(6), 1044-1056 (2009).
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1044-1056
    • Brunner, A.L.1    Johnson, D.S.2    Kim, S.W.3
  • 32
    • 68249105690 scopus 로고    scopus 로고
    • Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
    • Li JB, Gao Y, Aach J et al.: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 19(9), 1606-1615 (2009).
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1606-1615
    • Li, J.B.1    Gao, Y.2    Aach, J.3
  • 33
  • 34
    • 0035187518 scopus 로고    scopus 로고
    • Promoter methylation ana lysis on microdissected paraffn-embedded tissues using bisulfte treatment and PCR-SSCP
    • Bian YS, Yan P, Osterheld MC, Fontolliet C, Benhattar J: Promoter methylation ana lysis on microdissected paraffn-embedded tissues using bisulfte treatment and PCR-SSCP. BioTechniques 30(1), 66-72 (2001).
    • (2001) BioTechniques , vol.30 , Issue.1 , pp. 66-72
    • Bian, Y.S.1    Yan, P.2    Osterheld, M.C.3    Fontolliet, C.4    Benhattar, J.5
  • 35
    • 65849458558 scopus 로고    scopus 로고
    • Genome-wide massively parallel sequencing of formaldehyde fxed-paraffn embedded (FFPE) tumor tissues for copy-number-and mutation-ana lysis
    • Schweiger MR, Kerick M, Timmermann B et al.: Genome-wide massively parallel sequencing of formaldehyde fxed-paraffn embedded (FFPE) tumor tissues for copy-number-and mutation-ana lysis. PLoS ONE 4(5), E5548 (2009).
    • (2009) PLoS ONE , vol.4 , Issue.5
    • Schweiger, M.R.1    Kerick, M.2    Timmermann, B.3
  • 37
    • 0037137519 scopus 로고    scopus 로고
    • A gene-expression signature as a predictor of survival in breast cancer
    • Van De Vijver MJ, He YD, Van't Veer LJ et al.: A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347(25), 1999-2009 (2002).
    • (2002) N. Engl. J. Med , vol.347 , Issue.25 , pp. 1999-2009
    • Van De Vijver, M.J.1    He, Y.D.2    Van'T Veer, L.J.3
  • 38
    • 33846854438 scopus 로고    scopus 로고
    • The expanding role of epigenetics in the development, diagnosis and treatment of prostate cancer and benign prostatic hyperplasia
    • Dobosy JR, Roberts JL, Fu VX, Jarrard DF: The expanding role of epigenetics in the development, diagnosis and treatment of prostate cancer and benign prostatic hyperplasia. J. Urol. 177(3), 822-831 (2007).
    • (2007) J. Urol , vol.177 , Issue.3 , pp. 822-831
    • Dobosy, J.R.1    Roberts, J.L.2    Fu, V.X.3    Jarrard, D.F.4
  • 39
    • 70249089090 scopus 로고    scopus 로고
    • Single-molecule sequencing of an individual human genome
    • Pushkarev D, Neff NF, Quake SR: Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 27(9), 847-852 (2009).
    • (2009) Nat. Biotechnol , vol.27 , Issue.9 , pp. 847-852
    • Pushkarev, D.1    Neff, N.F.2    Quake, S.R.3
  • 40
    • 73449139811 scopus 로고    scopus 로고
    • Scanning probe and nanopore DNA sequencing: Core techniques and possibilities
    • Lund J, Parviz BA: Scanning probe and nanopore DNA sequencing: core techniques and possibilities. Methods Mol. Biol. 578, 113-122 (2009).
    • (2009) Methods Mol. Biol , vol.578 , pp. 113-122
    • Lund, J.1    Parviz, B.A.2
  • 41
    • 53649108801 scopus 로고    scopus 로고
    • The potential and challenges of nanopore sequencing
    • Branton D, Deamer DW, Marziali A et al.: The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26(10), 1146-1153 (2008).
    • (2008) Nat. Biotechnol , vol.26 , Issue.10 , pp. 1146-1153
    • Branton, D.1    Deamer, D.W.2    Marziali, A.3


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