Kamalakaran, S., Kendall, J. T., Zhao, X., Tang, C., Khan, S., Ravi, K., Auletta, T., Riggs, M., Wang, Y., Helland, A., Naume, Bj., Dimitrova, N., Borresen-Dale, A.. L., Hicks, J. B., Lucito, R. (July 2009) Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation. Nucl. Acids Res., 37 (12). e89.
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Abstract
Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non-associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25 000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter-associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > CpG islands |
| CSHL Authors: | |
| Communities: | CSHL labs > Hicks lab CSHL labs > Lucito lab CSHL Cancer Center Shared Resources > Instrumentation Service |
| Depositing User: | Brian Soldo |
| Date: | July 2009 |
| Date Deposited: | 29 Mar 2012 14:37 |
| Last Modified: | 30 Dec 2014 16:54 |
| PMCID: | PMC2709589 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/25538 |
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