DNA methylation analysis by pyrosequencing (original) (raw)

References

  1. Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlén, M. & Nyrén, P. Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242, 84–89 (1996).
    Article CAS PubMed Google Scholar
  2. Ronaghi, M., Uhlén, M. & Nyrén, P. A sequencing method based on real-time pyrophosphate. Science 281 363, 365 (1998).
    Article CAS PubMed Google Scholar
  3. Langaee, T. & Ronaghi, M. Genetic variation analyses by Pyrosequencing. Mutat. Res. 573, 96–102 (2005).
    Article CAS PubMed Google Scholar
  4. Ogino, S. et al. Sensitive sequencing method for KRAS mutation detection by Pyrosequencing. J. Mol. Diagn. 7, 413–421 (2005).
    Article CAS PubMed PubMed Central Google Scholar
  5. Clarke, S.C. Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications. Expert Rev. Mol. Diagn. 5, 947–953 (2005).
    Article CAS PubMed Google Scholar
  6. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
    Article CAS PubMed PubMed Central Google Scholar
  7. Rickert, A.M., Premstaller, A., Gebhardt, C. & Oefner, P.J. Genotyping of Snps in a polyploid genome by pyrosequencing. Biotechniques 32, 592–593, 596–598, 600 passim (2002).
    Article CAS PubMed Google Scholar
  8. Gruber, J.D., Colligan, P.B. & Wolford, J.K. Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Hum. Genet. 110, 395–401 (2002).
    Article CAS PubMed Google Scholar
  9. Lavebratt, C. & Sengul, S. Single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools using pyrosequencing. Nat. Protoc. 1, 2573–2582 (2006).
    Article CAS PubMed Google Scholar
  10. Pielberg, G., Day, A.E., Plastow, G.S. & Andersson, L. A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res. 13, 2171–2177 (2003).
    Article CAS PubMed PubMed Central Google Scholar
  11. Deutsch, S. et al. Detection of aneuploidies by paralogous sequence quantification. J. Med. Genet. 41, 908–915 (2004).
    Article CAS PubMed PubMed Central Google Scholar
  12. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
    Article CAS PubMed Google Scholar
  13. Jones, P.A. & Baylin, S.B. The epigenomics of cancer. Cell 128, 683–692 (2007).
    Article CAS PubMed PubMed Central Google Scholar
  14. Laird, P.W. Early detection: the power and the promise of DNA methylation markers. Nat. Rev. Cancer 3, 253–266 (2003).
    Article CAS PubMed Google Scholar
  15. Brena, R.M., Huang, T.H. & Plass, C. Quantitative assessment of DNA methylation: potential applications for disease diagnosis, classification, and prognosis in clinical settings. J. Mol. Med. 84, 365–377 (2006).
    Article CAS PubMed Google Scholar
  16. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc. Natl. Acad. Sci. USA 102, 15785–15790 (2005).
    Article CAS PubMed Google Scholar
  17. Colella, S., Shen, L., Baggerly, K.A., Issa, J.P. & Krahe, R. Sensitive and quantitative universal pyrosequencing methylation analysis of CpG sites. Biotechniques 35, 146–150 (2003).
    Article CAS PubMed Google Scholar
  18. Tost, J., Dunker, J. & Gut, I.G. Analysis and quantification of multiple methylation variable positions in CpG islands by pyrosequencing. Biotechniques 35, 152–156 (2003).
    Article CAS PubMed Google Scholar
  19. Uhlmann, K., Brinckmann, A., Toliat, M.R., Ritter, H. & Nürnberg, P. Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis 23, 4072–4079 (2002).
    Article CAS PubMed Google Scholar
  20. Tost, J., El Abdalaoui, H. & Gut, I.G. Serial pyrosequencing for quantitative DNA methylation analysis. Biotechniques 40, 721–722, 724, 726 (2006).
    Article CAS PubMed Google Scholar
  21. Mirmohammadsadegh, A. et al. Epigenetic silencing of the PTEN gene in melanoma. Cancer Res. 66, 6546–6552 (2006).
    Article CAS PubMed Google Scholar
  22. Xinarianos, G. et al. Frequent genetic and epigenetic abnormalities contribute to the deregulation of cytoglobin in non-small cell lung cancer. Hum. Mol. Genet. 15, 2038–2044 (2006).
    Article CAS PubMed Google Scholar
  23. Schatz, P., Dietrich, D. & Schuster, M. Rapid analysis of CpG methylation patterns using RNase T1 cleavage and MALDI-TOF. Nucleic Acids Res. 32, e167 (2004).
    Article PubMed PubMed Central Google Scholar
  24. Yang, A.S. et al. DNA methylation changes after 5-aza-2′-deoxycytidine therapy in patients with leukemia. Cancer Res. 66, 5495–5503 (2006).
    Article CAS PubMed Google Scholar
  25. White, H.E., Durston, V.J., Harvey, J.F. & Cross, N.C. Quantitative analysis of SNRPN (correction of SNRPN) gene methylation by pyrosequencing as a diagnostic test for Prader-Willi syndrome and Angelman syndrome. Clin. Chem. 52, 1005–1013 (2006).
    Article CAS PubMed Google Scholar
  26. Wong, H.L. et al. Rapid and quantitative method of allele-specific DNA methylation analysis. Biotechniques 41, 734–739 (2006).
    Article CAS PubMed Google Scholar
  27. Yang, A.S. et al. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res. 32, e38 (2004).
    Article PubMed PubMed Central Google Scholar
  28. Karimi, M. et al. LUMA (LUminometric Methylation Assay)—a high throughput method to the analysis of genomic DNA methylation. Exp. Cell Res. 312, 1989–1995 (2006).
    Article CAS PubMed Google Scholar
  29. Li, L.C. & Dahiya, R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 18, 1427–1431 (2002).
    Article CAS PubMed Google Scholar
  30. Arányi, T., Váradi, A., Simon, I. & Tusnády, G.E. The BiSearch web server. BMC Bioinformatics 7, 431 (2006).
    Article PubMed PubMed Central Google Scholar
  31. Olek, A., Oswald, J. & Walter, J. A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res. 24, 5064–5066 (1996).
    Article CAS PubMed PubMed Central Google Scholar
  32. Boyd, V.L. & Zon, G. 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 (2004).
    Article CAS PubMed Google Scholar
  33. Bian, Y.S., Yan, P., Osterheld, M.C., Fontolliet, C. & Benhattar, J. Promoter methylation analysis on microdissected paraffin-embedded tissues using bisulfite treatment and PCR-SSCP. Biotechniques 30, 66–72 (2001).
    Article CAS PubMed Google Scholar
  34. Kerjean, A. et al. Bisulfite genomic sequencing of microdissected cells. Nucleic Acids Res. 29, e106 (2001).
    Article CAS PubMed PubMed Central Google Scholar
  35. Shiraishi, M. & Hayatsu, H. High-speed conversion of cytosine to uracil in bisulfite genomic sequencing analysis of DNA methylation. DNA Res. 11, 409–415 (2004).
    Article CAS PubMed Google Scholar
  36. Dupont, J.M., Tost, J., Jammes, H. & Gut, I.G. De novo quantitative bisulfite sequencing using the pyrosequencing technology. Anal. Biochem. 333, 119–127 (2004).
    Article CAS PubMed Google Scholar
  37. Warnecke, P.M. et al. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res. 25, 4422–4426 (1997).
    Article CAS PubMed PubMed Central Google Scholar
  38. Wojdacz, T.K. & Hansen, L.L. Reversal of PCR bias for improved sensitivity of the DNA methylation melting curve assay. Biotechniques 41 274, 276, 278 (2006).
    Article CAS PubMed Google Scholar
  39. Shen, L., Guo, Y., Chen, X., Ahmed, S. & Issa, J.P. Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. Biotechniques 42, 48–52 (2007).
    Article CAS PubMed Google Scholar

Download references