Comparison of Methylation Density In Different Cancer Types By HumanMethylation450 Methods

Abnormal hypermethylation of DNA is highly detected in many cancer types. It is accepted that the hypermethylation contributes to tumor developing by silencing the tumor suppressor genes expression. New data techniques, Illumina Infinium HumanMethylation450, gives us a wide approach about genome methylation density and location. 8 different TCGA cancer data were compared. As a result, hypomethylated and hypermethylated genes were selected. Moreover, the highest methylated chromosomes, such as 19, 16, 17, 7, 11, 1, have been detected among the cancer types. The lowest and the highest beta value of the genes and chromosomes may give us a methylation range to understand future methylation process. Physical map of hypermethylated, near the both ends of chromosomes, and hypomethylated genes, near the centromere, is another result of this paper.

[1]  H. Spencer,et al.  A census of mammalian imprinting. , 2005, Trends in genetics : TIG.

[2]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[3]  C. Walsh,et al.  Cytosine methylation and the ecology of intragenomic parasites. , 1997, Trends in genetics : TIG.

[4]  Bernhard Korn,et al.  Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. , 2011, American journal of human genetics.

[5]  Zheng Guo,et al.  Reproducibility and Concordance of Differential DNA Methylation and Gene Expression in Cancer , 2012, PloS one.

[6]  Jian-Bing Fan,et al.  GoldenGate assay for DNA methylation profiling. , 2009, Methods in molecular biology.

[7]  A. Feinberg,et al.  The history of cancer epigenetics , 2004, Nature Reviews Cancer.

[8]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[9]  Peter A. Jones,et al.  The fundamental role of epigenetic events in cancer , 2002, Nature Reviews Genetics.

[10]  P. Laird.  Principles and challenges of genome-wide DNA methylation analysis , 2010, Nature Reviews Genetics.

[11]  Carolyn J. Brown,et al.  Silencing of the mammalian X chromosome. , 2005, Annual review of genomics and human genetics.

[12]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[13]  W Dean,et al.  Mammalian epigenomics: reprogramming the genome for development and therapy. , 2003, Theriogenology.

[14]  Stephan Beck,et al.  Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus , 2010, BMC Medical Genomics.

[15]  Hanna Göransson,et al.  Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. , 2010, Blood.

[16]  A. Oshlack,et al.  SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips , 2012, Genome Biology.

[17]  Colm E. Nestor,et al.  Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns , 2012, Genome Biology.

[18]  E. Birney,et al.  An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). , 2008, Genome research.