Methods for genome-wide DNA methylation analysis in human cancer

Abstract

Aberrant DNA methylation is considered to be one of themost common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNAmethylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide DNAmethylation, and the available cancerassociatedmethylation databases. Additionally, we focus on the computationalmethods for preprocessing, analyzing and interpreting the cancermethylome data. It not only discusses the challenges of the differentiallymethylated region calling and the predictionmodel construction but also highlights the biomarker investigation for cancer diagnosis, prognosis and response to treatment. Finally, some emerging challenges in the computational analysis of cancermethylome data are summarized.