← Back to Search
Emerging Methods For Analysis Of The Cancer Methylome.
J. W. Chang, T. Huang, Yi-Ching Wang
Published 2008 · Biology, Medicine
Download PDFAnalyze on Scholarcy
CpG island hypermethylation plays a key role in the silencing of cancer-related genes. In recent years, some new and effective methods have been developed for high-throughput analysis of DNA methylation, and have provided DNA methylation markers as powerful tools for the development of innovative diagnostic and therapeutic strategies in cancer. In this review, we describe various current and emerging technologies for studying the DNA methylation profile in cancer including: the isoschizomers and gel-based methylation analysis, the microarray-based methylation analysis and the sequencing-based methylation analysis. All of these techniques have advantages and disadvantages, such as sensitivity, specificity, analysis scale and cost. In the coming years, newer platforms of low cost, high-throughput and greater expediency, and speed for cancer methylome analysis will be developed.
This paper references
DNA methylation markers of surfactant proteins in lung cancer.
Z. Lin (2007)
Genome-wide analysis of DNA methylation patterns
D. Zilberman (2007)
Cancer epigenomics: DNA methylomes and histone-modification maps
M. Esteller (2007)
Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas.
W. Gao (2008)
CpG island methylator phenotype in cancer
J. Issa (2004)
Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis.
R. Gitan (2002)
Differential distribution of DNA methylation within the RASSF1A CpG island in breast cancer.
P. Yan (2003)
Role for DNA methylation in genomic imprinting
E. Li (1993)
Expressed CpG island sequence tag microarray for dual screening of DNA hypermethylation and gene silencing in cancer cells.
H. Shi (2002)
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
M. Weber (2005)
Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours
M. Esteller (2002)
MMASS: an optimized array-based method for assessing CpG island methylation
A. Ibrahim (2006)
Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
Jonghwan Kim (2005)
Genome sequencing in microfabricated high-density picolitre reactors
M. Margulies (2005)
DNA methylation and ovarian cancer. I. Analysis of CpG island hypermethylation in human ovarian cancer using differential methylation hybridization.
A. Ahluwalia (2001)
D. Bentley (2006)
Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification.
M. Toyota (1999)
DNA methylation errors and cancer.
P. Jones (1996)
The methylome: approaches for global DNA methylation profiling.
S. Beck (2008)
MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells.
T. Rauch (2006)
A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer
H. Suzuki (2002)
Genome-wide profiling of promoter methylation in human
I. Hatada (2006)
Purification of CpG islands using a methylated DNA binding column
S. Cross (1994)
Genome-wide promoter analysis uncovers portions of the cancer methylome.
M. Hoque (2008)
Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells.
F. V. Jacinto (2007)
Genome-wide identification of aberrantly methylated promoter associated CpG islands in acute lymphocytic leukemia
S-Q Kuang (2008)
Comprehensive high-throughput arrays for relative methylation (CHARM).
R. Irizarry (2008)
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing.
K. Taylor (2007)
Comparative isoschizomer profiling of cytosine methylation: the HELP assay.
B. Khulan (2006)
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
M. Frommer (1992)
MUC1 expression is regulated by DNA methylation and histone H3 lysine 9 modification in cancer cells.
N. Yamada (2008)
Identification of DNA Methylation in 3' Genomic Regions that are Associated with Upregulation of Gene Expression in Colorectal Cancer
J. F. Smith (2007)
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Shawn Cokus (2008)
Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation.
C. Nguyen (2001)
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines
C. Mund (2005)
High-Resolution Profiling of Histone Methylations in the Human Genome
A. Barski (2007)
Aberrant CpG-island methylation has non-random and tumour-type–specific patterns
J. Costello (2000)
Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry.
M. Ehrich (2005)
Genome-scale DNA methylation maps of pluripotent and differentiated cells
A. Meissner (2008)
Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets.
J. Ordway (2006)
Methyl‐CpG binding proteins identify novel sites of epigenetic inactivation in human cancer
E. Ballestar (2003)
S‐Adenosylmetliionine and methylation
P. Chiang (1996)
Role of transposable elements in heterochromatin and epigenetic control
Z. Lippman (2004)
Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA.
Y. Korshunova (2008)
Evidence for an instructive mechanism of de novo methylation in cancer cells
I. Keshet (2006)
Microarray-based molecular margin methylation pattern analysis in colorectal carcinoma.
D. Zhang (2006)
Epigenomic Changes during Leukemia Cell Differentiation: Analysis of Histone Acetylation and Cytosine Methylation Using CpG Island Microarrays
M. Nouzova (2004)
Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation.
P. Yan (2002)
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
R. Lister (2008)
Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors.
H. Bjornsson (2007)
High-throughput DNA methylation profiling using universal bead arrays.
M. Bibikova (2006)
Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates
J. Lewin (2004)
High-throughput methylation profiling by MCA coupled to CpG island microarray.
M. Estécio (2007)
Dependence of histone modifications and gene expression on DNA hypermethylation in cancer.
J. A. Fahrner (2002)
A blueprint for a Human Epigenome Project: the AACR Human Epigenome Workshop.
P. Jones (2005)
Methylation profiling of CpG islands in human breast cancer cells.
T. Huang (1999)
DNA methylation profiling of human chromosomes 6, 20 and 22
Florian Eckhardt (2006)
Profiling DNA methylation patterns using genomic tiling microarrays
Z. Lippman (2005)
DNA hypermethylation in tumorigenesis: epigenetics joins genetics.
S. Baylin (2000)
Pharmacologic unmasking of epigenetically silenced tumor suppressor genes in esophageal squamous cell carcinoma.
K. Yamashita (2002)
Genetic unmasking of epigenetically silenced tumor suppressor genes in colon cancer cells deficient in DNA methyltransferases.
M. Paz (2003)
CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer
T. Huang (1999)
This paper is referenced by
Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers
Ekaterina Olkhov-Mitsel (2012)
Impact of Sample Heterogeneity on Methylation Analysis
M. Loh (2010)
Immunohistochemistry and molecular diagnostics of pleural malignant mesothelioma.
P. Betta (2012)
Diagnostic molecular biomarkers for malignant pleural effusions.
K. Sriram (2011)
Molecular Profiling Methods in the Diagnosis of Hematologic Disorders
Annette S. Kim (2012)
Profiling DNA Methylomes from Microarray to Genome-Scale Sequencing
Yi-Wei Huang (2010)
Chromatin remodeling in mammary gland differentiation and breast tumorigenesis.
T. Huang (2010)
Hypomethylation of repeated DNA sequences in cancer.
J. Ross (2010)
Detection of genomic DNA methylation with denaturing high performance liquid chromatography
R. Omaruddin (2011)