A Review of the Methods for Detecting and Characterizing DNA Methylation as a Cancer Biomark

Abstract

DNA methylation is a covalent alteration in the DNA genome that modifies the expression of gene. DNA methylation occurs by adding methyl group to DNA molecule at fifth carbon of Cytosine ring. This process alters DNA activities but doesn’t change the sequence. This modification may cause tumorigenesis and cancer progression. Therefore, there is an urgently need to detect the methylated sites in DNA sequences and their regulation mechanisms which effect the epigenetics transformation. Predominantly, these epigenetic changes are in small regions in DNA called CpG islands, which exist with various frequencies in DNA sequences but mostly detected in promoter regions. Recently, a lot of efforts have been dedicated to computationally detect CpG islands, build large-scaled databases with visualization tools and develop analysis methods for DNA methylation data. Here, we provide a review on CpG islands detectors and classifier algorithms. We focus on genome-wide methylation databases of human cancers. We present an overview of methodologies available for DNA deferential methylation analysis. We aimed to summarize the recent efforts in DNA methylation changes and their significance in human cancers to open the door for more development in mechanisms and treatment perspectives.