Transcriptomics

Dataset Information

2

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2


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. We have developed a method to profile genome wide methylation. 7 ovarian normal samples and 11 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method.

ORGANISM(S): Homo sapiens  

SUBMITTER: Michael Riggs   Chunlao Tang  Robert Lucito  James Hicks  James Byrnes  Sitharthan Kamalakaran 

PROVIDER: E-GEOD-15747 | ArrayExpress | 2010-05-19

SECONDARY ACCESSION(S): GSE15747PRJNA123033

REPOSITORIES: GEO, ArrayExpress

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Publications

Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.

Kamalakaran Sitharthan S   Kendall Jude J   Zhao Xiaoyue X   Tang Chunlao C   Khan Sohail S   Ravi Kandasamy K   Auletta Theresa T   Riggs Michael M   Wang Yun Y   Helland Aslaug A   Naume Bjørn B   Dimitrova Nevenka N   Børresen-Dale Anne-Lise AL   Hicks Jim J   Lucito Robert R  

Nucleic acids research 20090527 12


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  ...[more]

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