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Volumn 9, Issue 4, 2014, Pages

Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; THYMINE; DIAGNOSTIC KIT; DNA; HYDROGEN SULFITE; SULFITE;

EID: 84899444670     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0093933     Document Type: Article
Times cited : (116)

References (40)
  • 1
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 13: 484-492.
    • (2012) Nat Rev Genet , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 2
    • 84875745673 scopus 로고    scopus 로고
    • Interplay between the cancer genome and epigenome
    • Shen H, Laird PW (2013) Interplay between the cancer genome and epigenome. Cell. 153: 38-55.
    • (2013) Cell , vol.153 , pp. 38-55
    • Shen, H.1    Laird, P.W.2
  • 3
    • 0034626988 scopus 로고    scopus 로고
    • Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents
    • Esteller M, Garcia-Foncillas J, Andion E, Goodman SN, Hidalgo OF, et al. (2000) Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med. 343: 1350-1354.
    • (2000) N Engl J Med , vol.343 , pp. 1350-1354
    • Esteller, M.1    Garcia-Foncillas, J.2    Andion, E.3    Goodman, S.N.4    Hidalgo, O.F.5
  • 5
    • 84873722466 scopus 로고    scopus 로고
    • Clinical utility of an epigenetic assay to detect occult prostate cancer in histopathologically negative biopsies: Results of the MATLOC study
    • Stewart GD, Van Neste L, Delvenne P, Delrée P, Delga A, et al. (2013) Clinical utility of an epigenetic assay to detect occult prostate cancer in histopathologically negative biopsies: results of the MATLOC study. J Urol. 189: 1110-1116.
    • (2013) J Urol , vol.189 , pp. 1110-1116
    • Stewart, G.D.1    Van Neste, L.2    Delvenne, P.3    Delrée, P.4    Delga, A.5
  • 6
    • 77953123406 scopus 로고    scopus 로고
    • Multicenter clinical validation of PITX2 methylation as a prostate specific antigen recurrence predictor in patients with post-radical prostatectomy prostate cancer
    • Bañez LL, Sun L, van Leenders GJ, Wheeler TM, Bangma CH, et al. (2010) Multicenter clinical validation of PITX2 methylation as a prostate specific antigen recurrence predictor in patients with post-radical prostatectomy prostate cancer. J Urol. 184: 149-156.
    • (2010) J Urol , vol.184 , pp. 149-156
    • Bañez, L.L.1    Sun, L.2    Van Leenders, G.J.3    Wheeler, T.M.4    Bangma, C.H.5
  • 7
    • 84874527353 scopus 로고    scopus 로고
    • Development and clinical validation of a real-time PCR assay for PITX2 DNA methylation to predict prostate-specific antigen recurrence in prostate cancer patients following radical prostatectomy
    • Dietrich D, Hasinger O, Bañez LL, Sun L, van Leenders GJ, et al. (2013) Development and clinical validation of a real-time PCR assay for PITX2 DNA methylation to predict prostate-specific antigen recurrence in prostate cancer patients following radical prostatectomy. J Mol Diagn. 15: 270-279.
    • (2013) J Mol Diagn , vol.15 , pp. 270-279
    • Dietrich, D.1    Hasinger, O.2    Bañez, L.L.3    Sun, L.4    Van Leenders, G.J.5
  • 8
    • 62349136443 scopus 로고    scopus 로고
    • DNA methylation of the PITX2 gene promoter region is a strong independent prognostic marker of biochemical recurrence in patients with prostate cancer after radical prostatectomy
    • Weiss G, Cottrell S, Distler J, Schatz P, Kristiansen G, et al. (2009) DNA methylation of the PITX2 gene promoter region is a strong independent prognostic marker of biochemical recurrence in patients with prostate cancer after radical prostatectomy. J Urol. 181: 1678-1685.
    • (2009) J Urol , vol.181 , pp. 1678-1685
    • Weiss, G.1    Cottrell, S.2    Distler, J.3    Schatz, P.4    Kristiansen, G.5
  • 9
    • 77951747373 scopus 로고    scopus 로고
    • Development of a diagnostic microarray assay to assess the risk of recurrence of prostate cancer based on PITX2 DNA methylation
    • Schatz P, Dietrich D, Koenig T, Burger M, Lukas A, et al. (2010) Development of a diagnostic microarray assay to assess the risk of recurrence of prostate cancer based on PITX2 DNA methylation. J Mol Diagn. 12: 345-353.
    • (2010) J Mol Diagn , vol.12 , pp. 345-353
    • Schatz, P.1    Dietrich, D.2    Koenig, T.3    Burger, M.4    Lukas, A.5
  • 10
    • 84891743167 scopus 로고    scopus 로고
    • Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer
    • Church TR, Wandell M, Lofton-Day C, Mongin SJ, Burger M, et al. (2014) Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer. Gut. 63: 317-325.
    • (2014) Gut , vol.63 , pp. 317-325
    • Church, T.R.1    Wandell, M.2    Lofton-Day, C.3    Mongin, S.J.4    Burger, M.5
  • 11
    • 80052967970 scopus 로고    scopus 로고
    • SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma
    • Kneip C, Schmidt B, Seegebarth A, Weickmann S, Fleischhacker M, et al. (2011) SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer in plasma. J Thorac Oncol. 6: 1632-1638.
    • (2011) J Thorac Oncol , vol.6 , pp. 1632-1638
    • Kneip, C.1    Schmidt, B.2    Seegebarth, A.3    Weickmann, S.4    Fleischhacker, M.5
  • 12
    • 78049345913 scopus 로고    scopus 로고
    • SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates
    • Schmidt B, Liebenberg V, Dietrich D, Schlegel T, Kneip C, et al. (2010) SHOX2 DNA methylation is a biomarker for the diagnosis of lung cancer based on bronchial aspirates. BMC Cancer. 10: 600.
    • (2010) BMC Cancer , vol.10 , pp. 600
    • Schmidt, B.1    Liebenberg, V.2    Dietrich, D.3    Schlegel, T.4    Kneip, C.5
  • 13
    • 84857159930 scopus 로고    scopus 로고
    • Performance evaluation of the DNA methylation biomarker SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates
    • Dietrich D, Kneip C, Raji O, Liloglou T, Seegebarth A, et al. (2012) Performance evaluation of the DNA methylation biomarker SHOX2 for the aid in diagnosis of lung cancer based on the analysis of bronchial aspirates. Int J Oncol. 40: 825-832.
    • (2012) Int J Oncol , vol.40 , pp. 825-832
    • Dietrich, D.1    Kneip, C.2    Raji, O.3    Liloglou, T.4    Seegebarth, A.5
  • 15
    • 84893547259 scopus 로고    scopus 로고
    • Diagnostic and Prognostic Value of SHOX2 and SEPT9 DNA Methylation and Cytology in Benign, Paramalignant and Malignant Pleural Effusions
    • Dietrich D, Jung M, Puetzer S, Leisse A, Holmes EE, et al. (2013) Diagnostic and Prognostic Value of SHOX2 and SEPT9 DNA Methylation and Cytology in Benign, Paramalignant and Malignant Pleural Effusions. PLoS One. 8: e84225.
    • (2013) PLoS One , vol.8
    • Dietrich, D.1    Jung, M.2    Puetzer, S.3    Leisse, A.4    Holmes, E.E.5
  • 16
    • 84887034056 scopus 로고    scopus 로고
    • Assessment of SHOX2 methylation in EBUS-TBNA specimen improves accuracy in lung cancer staging
    • Darwiche K, Zarogoulidis P, Baehner K, Welter S, Tetzner R, et al. (2013) Assessment of SHOX2 methylation in EBUS-TBNA specimen improves accuracy in lung cancer staging. Ann Oncol. 24: 2866-2870.
    • (2013) Ann Oncol , vol.24 , pp. 2866-2870
    • Darwiche, K.1    Zarogoulidis, P.2    Baehner, K.3    Welter, S.4    Tetzner, R.5
  • 17
    • 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, Collis CM, Watt F, et al. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 89: 1827-1831.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 1827-1831
    • Frommer, M.1    McDonald, L.E.2    Millar, D.S.3    Collis, C.M.4    Watt, F.5
  • 18
    • 77952967431 scopus 로고    scopus 로고
    • Direct detection of DNA methylation during single-molecule, real-time sequencing
    • Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, et al. (2010). Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 7: 461-465.
    • (2010) Nat Methods , vol.7 , pp. 461-465
    • Flusberg, B.A.1    Webster, D.R.2    Lee, J.H.3    Travers, K.J.4    Olivares, E.C.5
  • 20
    • 0036311221 scopus 로고    scopus 로고
    • Methylation sequencing from limiting DNA: Embryonic, fixed, and microdissected cells
    • DOI 10.1016/S1046-2023(02)00061-0, PII S1046202302000610
    • Millar DS, Warnecke PM, Melki JR, Clark SJ (2002) Methylation sequencing from limiting DNA: embryonic, fixed, and microdissected cells. Methods. 27: 108-113. (Pubitemid 34757120)
    • (2002) Methods , vol.27 , Issue.2 , pp. 108-113
    • Millar, D.S.1    Warnecke, P.M.2    Melki, J.R.3    Clark, S.J.4
  • 21
    • 1442323788 scopus 로고    scopus 로고
    • Bisulfite conversion of genomic DNA for methylation analysis: Protocol simplification with higher recovery applicable to limited samples and increased throughput
    • DOI 10.1016/j.ab.2003.11.020, PII S0003269703008315
    • Boyd VL, Zon G (2004) Bisulfite conversion of genomic DNA for methylation analysis: protocol simplification with higher recovery applicable to limited samples and increased throughput. Anal Biochem. 326: 278-280. (Pubitemid 38293391)
    • (2004) Analytical Biochemistry , vol.326 , Issue.2 , pp. 278-280
    • Boyd, V.L.1    Zon, G.2
  • 22
    • 36049007465 scopus 로고    scopus 로고
    • Accelerated bisulfite-deamination of cytosine in the genomic sequencing procedure for DNA methylation analysis
    • Hayatsu H, Negishi K, Shiraishi M (2004) Accelerated bisulfite- deamination of cytosine in the genomic sequencing procedure for DNA methylation analysis. Nucleic Acids Symp Ser (Oxf). 48: 261-262.
    • (2004) Nucleic Acids Symp Ser (Oxf) , vol.48 , pp. 261-262
    • Hayatsu, H.1    Negishi, K.2    Shiraishi, M.3
  • 24
    • 21044454727 scopus 로고    scopus 로고
    • High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation
    • DOI 10.1093/dnares/11.6.409
    • Shiraishi M, Hayatsu H (2004) High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation. DNA Res. 11: 409-415. (Pubitemid 40873615)
    • (2004) DNA Research , vol.11 , Issue.6 , pp. 409-415
    • Shiraishi, M.1    Hayatsu, H.2
  • 25
    • 84885408749 scopus 로고    scopus 로고
    • Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition
    • Dietrich D, Uhl B, Sailer V, Holmes EE, Jung M, et al. (2013) Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition. PLoS One. 8: e77771.
    • (2013) PLoS One , vol.8
    • Dietrich, D.1    Uhl, B.2    Sailer, V.3    Holmes, E.E.4    Jung, M.5
  • 26
    • 67650077151 scopus 로고    scopus 로고
    • Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer
    • deVos T, Tetzner R, Model F, Weiss G, Schuster M, et al. (2009) Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem. 55: 1337-1346.
    • (2009) Clin Chem , vol.55 , pp. 1337-1346
    • DeVos, T.1    Tetzner, R.2    Model, F.3    Weiss, G.4    Schuster, M.5
  • 27
    • 58749087364 scopus 로고    scopus 로고
    • Errors in the bisulfite conversion of DNA: Modulating inappropriate- and failed-conversion frequencies
    • Genereux DP, Johnson WC, Burden AF, Stöger R, Laird CD (2008) Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. Nucleic Acids Res. 36: e150.
    • (2008) Nucleic Acids Res , vol.36
    • Genereux, D.P.1    Johnson, W.C.2    Burden, A.F.3    Stöger, R.4    Laird, C.D.5
  • 28
    • 0036311202 scopus 로고    scopus 로고
    • Identification and resolution of artifacts in bisulfite sequencing
    • DOI 10.1016/S1046-2023(02)00060-9, PII S1046202302000609
    • Warnecke PM, Stirzaker C, Song J, Grunau C, Melki JR, et al. (2002) Identification and resolution of artifacts in bisulfite sequencing. Methods. 27: 101-107. (Pubitemid 34757119)
    • (2002) Methods , vol.27 , Issue.2 , pp. 101-107
    • Warnecke, P.M.1    Stirzaker, C.2    Song, J.3    Grunau, C.4    Melki, J.R.5    Clark, S.J.6
  • 29
    • 0028961759 scopus 로고
    • A bisulfite method of 5-methylcytosine mapping that minimizes template degradation
    • Raizis AM, Schmitt F, Jost JP (1995) A bisulfite method of 5-methylcytosine mapping that minimizes template degradation. Anal Biochem. 226: 161-166.
    • (1995) Anal Biochem , vol.226 , pp. 161-166
    • Raizis, A.M.1    Schmitt, F.2    Jost, J.P.3
  • 30
    • 0035407651 scopus 로고    scopus 로고
    • Bisulfite genomic sequencing: Systematic investigation of critical experimental parameters
    • Grunau C, Clark SJ, Rosenthal A (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res. 29: E65-65.
    • (2001) Nucleic Acids Res , vol.29
    • Grunau, C.1    Clark, S.J.2    Rosenthal, A.3
  • 31
    • 33847619360 scopus 로고    scopus 로고
    • Degradation of DNA by bisulfite treatment
    • DOI 10.1016/j.bmcl.2007.01.040, PII S0960894X07000911
    • Tanaka K, Okamoto A (2007) Degradation of DNA by bisulfite treatment. Bioorg Med Chem Lett. 17: 1912-1915. (Pubitemid 46367676)
    • (2007) Bioorganic and Medicinal Chemistry Letters , vol.17 , Issue.7 , pp. 1912-1915
    • Tanaka, K.1    Okamoto, A.2
  • 32
    • 47849128445 scopus 로고    scopus 로고
    • The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research
    • Hayatsu H (2008) The bisulfite genomic sequencing used in the analysis of epigenetic states, a technique in the emerging environmental genotoxicology research. Mutat Res. 659: 77-82.
    • (2008) Mutat Res , vol.659 , pp. 77-82
    • Hayatsu, H.1
  • 33
    • 84878058547 scopus 로고    scopus 로고
    • The conversion of protonated cytosine-SO3(-) to uracil-SO3(-): Insights into the novel induced hydrolytic deamination through bisulfite catalysis
    • Jin L, Wang W, Hu D, Lü J (2013) The conversion of protonated cytosine-SO3(-) to uracil-SO3(-): insights into the novel induced hydrolytic deamination through bisulfite catalysis. Phys Chem Chem Phys. 15: 9034-9042.
    • (2013) Phys Chem Chem Phys , vol.15 , pp. 9034-9042
    • Jin, L.1    Wang, W.2    Hu, D.3    Lü, J.4
  • 34
    • 84860140980 scopus 로고    scopus 로고
    • High quality DNA obtained with an automated DNA extraction method with 70+ year old formalin-fixed celloidin-embedded (FFCE) blocks from the indiana medical history museum
    • Niland EE, McGuire A, Cox MH, Sandusky GE (2012) High quality DNA obtained with an automated DNA extraction method with 70+ year old formalin-fixed celloidin-embedded (FFCE) blocks from the indiana medical history museum. Am J Transl Res. 4: 198-205.
    • (2012) Am J Transl Res , vol.4 , pp. 198-205
    • Niland, E.E.1    McGuire, A.2    Cox, M.H.3    Sandusky, G.E.4
  • 35
    • 84856108985 scopus 로고    scopus 로고
    • Influence of prolonged formalin fixation of tissue samples on the sensitivity of chromogenic in situ hybridization
    • Mostegl MM, Richter B, Dinhopl N, Weissenböck H (2011) Influence of prolonged formalin fixation of tissue samples on the sensitivity of chromogenic in situ hybridization. J Vet Diagn Invest. 23: 1212-1216.
    • (2011) J Vet Diagn Invest , vol.23 , pp. 1212-1216
    • Mostegl, M.M.1    Richter, B.2    Dinhopl, N.3    Weissenböck, H.4
  • 36
    • 77956910135 scopus 로고    scopus 로고
    • Multicentre validation study of nucleic acids extraction from FFPE tissues
    • Bonin S, Hlubek F, Benhattar J, Denkert C, Dietel M, et al. (2010) Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch. 457: 309-317.
    • (2010) Virchows Arch , vol.457 , pp. 309-317
    • Bonin, S.1    Hlubek, F.2    Benhattar, J.3    Denkert, C.4    Dietel, M.5
  • 37
    • 84870451374 scopus 로고    scopus 로고
    • Improved PCR amplification for molecular analysis using DNA from long-term preserved formalin-fixed, paraffin-embedded lung cancer tissue specimens
    • Taga M, Eguchi H, Shinohara T, Takahashi K, Ito R, et al. (2013) Improved PCR amplification for molecular analysis using DNA from long-term preserved formalin-fixed, paraffin-embedded lung cancer tissue specimens. Int J Clin Exp Pathol. 6: 76-79.
    • (2013) Int J Clin Exp Pathol , vol.6 , pp. 76-79
    • Taga, M.1    Eguchi, H.2    Shinohara, T.3    Takahashi, K.4    Ito, R.5
  • 38
    • 61349121505 scopus 로고    scopus 로고
    • Cell-free tumor DNA in blood plasma as a marker for circulating tumor cells in prostate cancer
    • Schwarzenbach H, Alix-Panabières C, Müller I, Letang N, Vendrell JP, et al. (2009) Cell-free tumor DNA in blood plasma as a marker for circulating tumor cells in prostate cancer. Clin Cancer Res. 15: 1032-1038.
    • (2009) Clin Cancer Res , vol.15 , pp. 1032-1038
    • Schwarzenbach, H.1    Alix-Panabières, C.2    Müller, I.3    Letang, N.4    Vendrell, J.P.5
  • 39
    • 0242362613 scopus 로고    scopus 로고
    • Use of magnetic beads for plasma cell-free DNA extraction: Toward automation of plasma DNA analysis for molecular diagnostics
    • Stemmer C, Beau-Faller M, Pencreac'h E, Guerin E, Schneider A, et al. (2003) Use of magnetic beads for plasma cell-free DNA extraction: toward automation of plasma DNA analysis for molecular diagnostics. Clin Chem. 49: 1953-1935.
    • (2003) Clin Chem , vol.49 , pp. 1953-11935
    • Stemmer, C.1    Beau-Faller, M.2    Pencreac'H, E.3    Guerin, E.4    Schneider, A.5
  • 40
    • 0035103448 scopus 로고    scopus 로고
    • Quantitation of genomic DNA in plasma and serum samples: Higher concentrations of genomic DNA found in serum than in plasma
    • DOI 10.1046/j.1537-2995.2001.41020276.x
    • Lee TH, Montalvo L, Chrebtow V, Busch MP (2001) Quantitation of genomic DNA in plasma and serum samples: higher concentrations of genomic DNA found in serum than in plasma. Transfusion. 41: 276-282. (Pubitemid 32220522)
    • (2001) Transfusion , vol.41 , Issue.2 , pp. 276-282
    • Lee, T.-H.1    Montalvo, L.2    Chrebtow, V.3    Busch, M.P.4


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