184
Views
16
CrossRef citations to date
0
Altmetric
Review

Methylation-sensitive high-resolution melting in the context of legislative requirements for validation of analytical procedures for diagnostic applications

Pages 39-47 | Published online: 09 Jan 2014

References

  • Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA103(5), 1412–1417 (2006).
  • Riggs AD. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell. Genet.14(1), 9–25 (1975).
  • Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development. Science187, 226–232 (1975).
  • Holliday R. A new theory of carcinogenesis. Br. J. Cancer40, 513–522 (1979).
  • Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature301, 89–92 (1983).
  • Feinberg AP, Vogelstein B. Hypomethylation of ras oncogenes in primary human cancers. Biochem. Biophys. Res. Commun.111, 47–54 (1983).
  • Ohtani-Fujita N, Fujita T, Aoike A, Osifchin NE, Robbins PD, Sakai T. CpG methylation inactivates the promoter activity of the human retinoblastoma tumor-suppressor gene. Oncogene8, 1063–1067 (1993).
  • deVos T, Tetzner R, Model F et al. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin. Chem.55(7), 1337–1346 (2009).
  • Gonzalgo ML, Pavlovich CP, Lee SM, Nelson WG. Prostate cancer detection by GSTP1 methylation analysis of postbiopsy urine specimens. Clin. Cancer Res.9(7), 2673–2677 (2003).
  • Brock MV, Hooker CM, Ota-Machida E et al. DNA methylation markers and early recurrence in stage I lung cancer. N. Engl. J. Med.358(11), 1118–1128 (2008).
  • Maier S, Nimmrich I, Koenig T et al. DNA-methylation of the homeodomain transcription factor PITX2 reliably predicts risk of distant disease recurrence in tamoxifen-treated, node-negative breast cancer patients – technical and clinical validation in a multi-centre setting in collaboration with the European Organisation for Research and Treatment of Cancer (EORTC) PathoBiology group. Eur. J. Cancer43(11), 1679–1686 (2007).
  • Nakayama M, Wada M, Harada T et al. Hypomethylation status of CpG sites at the promoter region and overexpression of the human MDR1 gene in acute myeloid leukemias. Blood92(11), 4296–4307 (1998).
  • Hegi ME, Diserens AC, Gorlia T et al.MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med.352(10), 997–1003 (2005).
  • Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet.8(4), 253–262 (2007).
  • Ng SF, Lin RC, Laybutt DR, Barres R, Owens JA, Morris MJ. Chronic high-fat diet in fathers programs beta-cell dysfunction in female rat offspring. Nature467(7318), 963–966 (2010).
  • Wojdacz TK, Hansen LL. Techniques used in studies of age-related DNA methylation changes. Ann. NY Acad. Sci.1067, 479–487 (2006).
  • Laird PW. Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet.11(3), 191–203 (2010).
  • Wojdacz TK, Dobrovic A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res.35(6), e41 (2007).
  • Wojdacz TK, Dobrovic A, Hansen LL. Methylation-sensitive high-resolution melting. Nat. Protoc.3(12), 1903–1908 (2008).
  • Hudson B, Upholt WB, Devinny J, Vinograd J. The use of an ethidium analogue in the dye-buoyant density procedure for the isolation of closed circular DNA: the variation of the superhelix density of mitochondrial DNA. Proc. Natl Acad. Sci. USA62(3), 813–820 (1969).
  • Worm J, Aggerholm A, Guldberg P. In-tube DNA methylation profiling by fluorescence melting curve analysis. Clin. Chem.47(7), 1183–1189 (2001).
  • Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem.49(6 Pt 1), 853–860 (2003).
  • Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev. Mol. Diagn.10(2), 219–240 (2010).
  • Reinert T, Modin C, Castano FM et al. Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin. Cancer Res.17(17), 5582–5592 (2011).
  • Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res.22(15), 2990–2997 (1994).
  • Wojdacz TK, Hansen LL, Dobrovic A. A new approach to primer design for the control of PCR bias in methylation studies. BMC Res. Notes1, 54 (2008).
  • Wojdacz TK, Borgbo T, Hansen LL. Primer design versus PCR bias in methylation independent PCR amplifications. Epigenetics4(4), 231–234 (2009).
  • Warnecke PM, Stirzaker C, Melki JR, Millar DS, Paul CL, Clark SJ. Detection and measurement of PCR bias in quantitative methylation analysis of bisulphite-treated DNA. Nucleic Acids Res.25(21), 4422–4426 (1997).
  • Wojdacz TK, Hansen LL. Reversal of PCR bias for improved sensitivity of the DNA methylation melting curve assay. BioTechniques41(3), 274, 276, 278 (2006).
  • Dahl C, Guldberg P. DNA methylation analysis techniques. Biogerontology4(4), 233–250 (2003).
  • Clark SJ, Statham A, Stirzaker C, Molloy PL, Frommer M. DNA methylation: bisulphite modification and analysis. Nat. Protoc.1(5), 2353–2364 (2006).
  • Wojdacz TK, Moller TH, Thestrup BB, Kristensen LS, Hansen LL. Limitations and advantages of MS-HRM and bisulfite sequencing for single locus methylation studies. Expert Rev. Mol. Diagn.10(5), 575–580 (2010).
  • Balic M, Pichler M, Strutz J et al. High quality assessment of DNA methylation in archival tissues from colorectal cancer patients using quantitative high-resolution melting analysis. J. Mol. Diagn.11(2), 102–108 (2009).
  • Stanzer S, Balic M, Strutz J et al. Rapid and reliable detection of LINE-1 hypomethylation using high-resolution melting analysis. Clin. Biochem.43(18), 1443–1448 (2010).
  • Heitzer E, Bambach I, Dandachi N, Horn M, Wolf P. PTCH promoter methylation at low level in sporadic basal cell carcinoma analysed by three different approaches. Exp. Dermatol.19(10), 926–928 (2010).
  • Wojdacz TK, Dobrovic A. Melting curve assays for DNA methylation analysis. Methods Mol. Biol.507, 229–240 (2009).
  • Dodge JE, List AF, Futscher BW. Selective variegated methylation of the p15 CpG island in acute myeloid leukemia. Int. J. Cancer78, 561–567 (1998).
  • Aggerholm A, Hokland P. DAP-kinase CpG island methylation in acute myeloid leukemia: methodology versus biology? Blood95, 2997–2999 (2000).
  • Versmold B, Felsberg J, Mikeska T et al. Epigenetic silencing of the candidate tumor suppressor gene PROX1 in sporadic breast cancer. Int. J. Cancer121(3), 547–554 (2007).
  • Mikeska T, Felsberg J, Hewitt CA, Dobrovic A. Analysing DNA methylation using bisulphite pyrosequencing. Methods Mol. Biol.791, 33–53 (2011).
  • Candiloro IL, Mikeska T, Hokland P, Dobrovic A. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics Chromatin1(1), 7 (2008).
  • Kristensen LS, Wojdacz TK, Thestrup BB, Wiuf C, Hager H, Hansen LL. Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM. BMC Cancer9(1), 453 (2009).
  • Candiloro IL, Mikeska T, Dobrovic A. Assessing combined methylation-sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation. Epigenetics6(4), 500–507 (2011).
  • Gudnason H, Dufva M, Bang DD, Wolff A. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Res.35(19), e127 (2007).
  • Oster B, Thorsen K, Lamy P et al. Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int. J. Cancer129(12), 2855–2866 (2011).
  • Adachi JI, Mishima K, Wakiya K et al. O (6)-methylguanine-DNA methyltransferase promoter methylation in 45 primary central nervous system lymphomas: quantitative assessment of methylation and response to temozolomide treatment. J. Neurooncol. doi:10.1007/s11060-011-0721-3 (2011) (Epub ahead of print).

Websites

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.