Identification of patterns of DNA methylation in higher order eukaryotes has become necessary through recognition that disease processes such as cancer can result from abnormal methylation patterns. Abnormal DNA methylation affecting the promoter region of genes can halt their expression, making DNA methylation a marker of gene inactivation. The explosion of studies involving changes in DNA methylation in the last 10 yr, particularly in the study of cancer, are largely the result of two factors: the increasing awareness of the importance of epigenetic silencing in cancer and the improvements in the techniques used to determine changes in DNA methylation. In this chapter, focus is made on the specific methods of how to perform bisulfite modification of DNA and polymerase chain reaction as well as nested methylation specific polymerase chain reaction, and discuss other techniques to evaluate DNA methylation along with the limitations inherent in each process.
