Methylation-Specific Oligonucleotide Microarray
Humana Press eBooksPublished 23 July 2004
Pearlly S. Yan, Susan Wei, Tim Hui-Ming Huang
Citations22
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
The methylation-specific oligonucleotide (MSO) microarray is a high-throughput approach capable of detecting DNA methylation in genes across several CpG sites and design criteria important to the interrogation of multiple C pG sites across several genes are focused on.
Abstract
The methylation-specific oligonucleotide (MSO) microarray is a high-throughput approach capable of detecting DNA methylation in genes across several CpG sites. Based on the bisulfite modification of DNA that converts unmethylated cytosines to uracil but leaves the 5'methylcytosine intact, the method utilizes short oligonucleotides corresponding to the methylated and unmethylated alleles as probes affixed on solid support and products amplified from bisulfite-treated DNA as targets for hybridization. MSO is suitable for examining a panel of genes across multiple clinical samples. This approach can generate a robust dataset for discovering profiles of gene methylation in cancer with aberrant DNA methylation in the neoplastic genome and widespread hypermethylation in tumor suppressor genes. MSO and other oligonucleotide-based arrays have been applied successfully for analyses of single genes and have been useful in delineating and predicting tumor subgroups using clustering methods. Here we focus on design criteria important to the interrogation of multiple CpG sites across several genes.
Keywords
Biochemistry, Genetics and Molecular Biology
Genes & DevelopmentDNA methylation patterns and epigenetic memory
7,001 Citations2002Adrian Bird
The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development.
Proceedings of the National Academy of SciencesMethylation-specific PCR: a novel PCR assay for methylation status of CpG islands.
5,669 Citations1996James G. Herman, Jeremy R. Graff +3 more
The use of MSP is demonstrated to identify promoter region hypermethylation changes associated with transcriptional inactivation in four important tumor suppressor genes (p16, p15, E-cadherin and von Hippel-Lindau) in human cancer.
Nature Reviews GeneticsThe fundamental role of epigenetic events in cancer
5,614 Citations2002Peter A. Jones, Stephen B. Baylin
This review discusses patterns of DNA methylation and chromatin structure in neoplasia and the molecular alterations that might cause them and/or underlie altered gene expression in cancer.
Proceedings of the National Academy of SciencesA genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
3,265 Citations1992Marianne Frommer, Louise E. McDonald +6 more
A genomic sequencing method is reported that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.
Nature GeneticsAberrant CpG-island methylation has non-random and tumour-type–specific patterns
1,356 Citations2000J Costello, Michael C. Frühwald +21 more
This report reports a global analysis of the methylation status of 1,184 unselected CpG islands in each of 98 primary human tumours using restriction landmark genomic scanning (RLGS), and estimates that an average of 600 C pG islands were aberrantly methylated in the tumours, including early stage tumours.
Nucleic Acids ResearchCOBRA: a sensitive and quantitative DNA methylation assay
1,189 Citations1997Zhongguo Xiong, Peter W. Laird
COBRA shows that methylation levels in the original DNA sample are represented by the relative amounts of digested and undigested PCR product in a linearly quantitative fashion across a wide spectrum of DNAmethylation levels.
PubMedIdentification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification.
470 Citations1999Minoru Toyota, Coty Ho +6 more
It is proposed that MCA is a useful technique to study methylation and to isolate CpG islands differentially methylated in cancer.
OncogeneDNA methylation and breast carcinogenesis
460 Citations2002Martin Widschwendter, Peter A. Jones
How DNA-methylation contributes to breast cancer features and suggestions about how these changes could be prevented, reverted or used as a ‘tag’ for early detection of breast cancer or, preferably, for detection of premalignant changes are offered.
Human Molecular GeneticsMethylation profiling of CpG islands in human breast cancer cells
428 Citations1999Tim H-M. Huang
This study provides evidence that, aside from random DNA-MTase action, additional cellular factors exist that govern aberrant methylation in breast cancer cells.
PubMedCpG island hypermethylation in human colorectal tumors is not associated with DNA methyltransferase overexpression.
396 Citations1999Cindy A. Eads, K. D. Danenberg +4 more
The results suggest that deregulation of DNA methyltransferase gene expression does not play a role in establishing tumor-specific abnormal DNA methylation patterns in human colorectal cancer.
Nucleic Acids ResearchTumour class prediction and discovery by microarray-based DNA methylation analysis
284 Citations2002Péter Adorján
The first microarray-based technique which allows genome-wide assessment of selected CpG dinucleotides as well as quantification of methylation at each site is developed, demonstrating that genome- wide analysis of methylated patterns combined with supervised and unsupervised machine learning techniques constitute a powerful novel tool to classify human cancers.
Genome ResearchMethylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis
281 Citations2001Raad S. Gitan, Huidong Shi +3 more
This proof-of-principle study shows that MSO microarray is a promising technique for mapping methylation changes in multiple CpG island loci and for generating epigenetic profiles in cancer.
PubMedDissecting complex epigenetic alterations in breast cancer using CpG island microarrays.
235 Citations2001Pearlly S. Yan, Chuan‐Mu Chen +5 more
The notion that hypermethylation of critical CpG island loci influences cancer development and produces distinct epigenetic signatures for particular tumor subtypes is supported.
PubMedDifferential distribution of DNA methylation within the RASSF1A CpG island in breast cancer.
119 Citations2003Pearlly S. Yan, Huidong Shi +6 more
Functional analysis indicates that increased density of RASSF1A promoter methylation is associated with altered chromatin, marked by a depletion of acetylated histones and methylated histone 3-lysine 4 and an enrichment of methylated chromatin in the studied area.
Journal of Cellular BiochemistryOligonucleotide‐based microarray for DNA methylation analysis: Principles and applications
113 Citations2002Huidong Shi, Sabine Maier +5 more
An oligonucleotide‐based microarray technique that is both versatile and sensitive in revealing hypermethylation in defined regions of the genome holds promise to monitor the outcome of various epigenetic therapies on cancer patients.
Analytical BiochemistryParallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays
37 Citations2002Robert P. Balog, Y Emi Ponce de Souza +9 more
A method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation and demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.