A microarray to analyze methylation patterns of p16(Ink4a) gene 5'-CpG islands

Aberrant DNA methylation of the CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation on the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so f...

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Bibliographic Details
Published in:Clinical biochemistry 2003-05, Vol.36 (3), p.197
Main Authors: Hou, Peng, Ji, Meiju, Liu, Zhengchun, Shen, Jiayao, Cheng, L u, He, Nongyue, Lu, Zuhong
Format: Article
Language:English
Subjects:
Base Sequence
CpG Islands - genetics
Cyclin-Dependent Kinase Inhibitor p16 - genetics
DNA Methylation
Humans
In Situ Hybridization, Fluorescence
Molecular Sequence Data
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Probes
Stomach Neoplasms - genetics
Stomach Neoplasms - metabolism
Sulfites
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Summary:Aberrant DNA methylation of the CpG site is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation on the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. However, large-scale analysis of candidate genes has so far been hampered by the lack of high throughput approach for analyzing methylation patterns. The aim of this study was to develop a new method to analyze methylation patterns of p16(Ink4a) gene. We selected a 336 bp segment of the 5' untranslated region and the first exon of the p16(Ink4a) gene, as the target sequence, which include the most densely packed CpG fragment of the islands containing 32 CpG sites. A set of oligonucleotide probes was designed to assemble a DNA microarray to discriminate the methylation patterns of several adjacent CpG sites. Methylation patterns of human p16(Ink4a) gene were mapped and the results were validated by bisulphite DNA sequencing. A good reproducibility was observed in several parallel experiments. The methylation oligonucleotide microarray can be applied as a useful and powerful tool to map methylation patterns in multiple CpG island sites.
ISSN:0009-9120
DOI:10.1016/S0009-9120(02)00445-9