Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.
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.
Kamalakaran
Sitharthan
S
Philips Research North America, Briarcliff Manor, NY 10510, USA.
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
D002460:Cell Line; D018899:CpG Islands; D019175:DNA Methylation; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*