Methylation specific oligonucleotide microarray
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Methylation specific oligonucleotide microarray was developed as a technique to map methylation changes in DNA in cancer. This technique was developed by Professor Tim Hui-Ming Huang and was published in journal Genome Research on 2002 (Gitan et al., 2002). The method utilizes bisulfite-modified DNA that is used as templates for PCR amplification, which is subsequently hybridized to oligonucleotide microarray.
Implications on Cancer Research
Cancer cells often develop atypical methylation patterns, at CpG sites in promoters of tumour suppressor genes. High levels of methylation at a promoter leads to downregulation of the corresponding genes and is characteristic of carcinogenesis. It is one of the most consistent changes observed in early stage tumour cells.[1] Methylation specific oligonucleotide microarray allows for the high resolution and high throughput detection of numerous methylation events on multiple gene promoters. Therefore, this technique can be used to detect aberrant methylation in tumour suppressor promoters at an early stage and has been used in gastric and colon cancers and multiple others.[2][3] Because it allows one to detect presence of atypical methylations in cancer cells, it can also be used to reveal the major cause behind the malignancy, whether its main contributor is mutations on chromosomes or epigenetic modifications, as well as which tumour suppressor genes' transcription levels are affected.[4][5] An interesting use of this microarray includes specific classification of cancers based on the methylation patterns alone, such as differentiating between classes of leukemia, suggesting that different classes of cancer show relatively unique methylation patterns.[6] This technique has also been proposed to monitor cancer treatments that involve modifying the methylation patterns in mutant cancer cells. [4]
External links
- Resources, information and specific protocols for DNA Methylation Analysis
- Software for DNA Methylation Analysis
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- ^ Gitan, Raad S.; Shi, Huidong; Chen, Chuan-Mu; Yan, Pearlly S.; Huang, Tim Hui-Ming (2002). "Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis". Genome Research. 12 (1): 158–164. doi:10.1101/gr.202801. ISSN 1088-9051. PMID 11779841.
- ^ Hou, Peng; Shen, Jia-Yao; Ji, Mei-Ju; He, Nong-Yue; Lu, Zu-Hong (2004-12-15). "Microarray-based method for detecting methylation changes of p16Ink4a gene 5'-CpG islands in gastric carcinomas". World Journal of Gastroenterology : WJG. 10 (24): 3553–3558. doi:10.3748/wjg.v10.i24.3553. ISSN 1007-9327. PMC 4611991. PMID 15534905.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Mund, Cora; Beier, Verena; Bewerunge, Peter; Dahms, Michael; Lyko, Frank; Hoheisel, Jörg D. (2005-04-28). "Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines". Nucleic Acids Research. 33 (8): e73. doi:10.1093/nar/gni072. ISSN 1362-4962. PMC 1087791. PMID 15860770.
- ^ a b Shi, Huidong; Maier, Sabine; Nimmrich, Inko; Yan, Pearlly S.; Caldwell, Charles W.; Olek, Alexander; Huang, Tim Hui-Ming (2003-01-01). "Oligonucleotide-based microarray for DNA methylation analysis: principles and applications". Journal of Cellular Biochemistry. 88 (1): 138–143. doi:10.1002/jcb.10313. ISSN 0730-2312. PMID 12461783.
- ^ Yu, Yan Ping; Paranjpe, Shirish; Nelson, Joel; Finkelstein, Sydney; Ren, Baoguo; Kokkinakis, Demetrius; Michalopoulos, George; Luo, Jian-Hua (2005). "High throughput screening of methylation status of genes in prostate cancer using an oligonucleotide methylation array". Carcinogenesis. 26 (2): 471–479. doi:10.1093/carcin/bgh310. ISSN 0143-3334.
- ^ Adorjan, P. (2002). "Tumour class prediction and discovery by microarray-based DNA methylation analysis". Nucleic Acids Research. 30 (5): 21e–21. doi:10.1093/nar/30.5.e21. PMC 101257. PMID 11861926.
{{cite journal}}: CS1 maint: PMC format (link)