title: Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation.
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.
authors.affiliation: Philips Research North America, Briarcliff Manor, NY 10510, USA.
authors.forename: Sitharthan
authors.initials: S
authors.lastname: Kamalakaran
authors.forename: Jude
authors.initials: J
authors.lastname: Kendall
authors.forename: Xiaoyue
authors.initials: X
authors.lastname: Zhao
authors.forename: Chunlao
authors.initials: C
authors.lastname: Tang
authors.forename: Sohail
authors.initials: S
authors.lastname: Khan
authors.forename: Kandasamy
authors.initials: K
authors.lastname: Ravi
authors.forename: Theresa
authors.initials: T
authors.lastname: Auletta
authors.forename: Michael
authors.initials: M
authors.lastname: Riggs
authors.forename: Yun
authors.initials: Y
authors.lastname: Wang
authors.forename: Aslaug
authors.initials: A
authors.lastname: Helland
authors.forename: Bjørn
authors.initials: B
authors.lastname: Naume
authors.forename: Nevenka
authors.initials: N
authors.lastname: Dimitrova
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.forename: Jim
authors.initials: J
authors.lastname: Hicks
authors.forename: Robert
authors.initials: R
authors.lastname: Lucito
mesh_terms: D002460:Cell Line; D018899:CpG Islands; D019175:DNA Methylation; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*