Batch effects in differential DNA methylation research

摘要

Hundreds of genes with differential DNA methylation of promoters have been identified for various cancers. However, the reproducibility of differential DNA methylation discoveries for cancer have not been systematically analysed. Here,using array data for nine types of cancers, we evaluated the effects of experimental batches on differential DNA methylation detection. The results showed batch effects could greatly affect the discovery of DNA methylation biomarkers. Then, we compared the directions of DNA methylation changes detected from different datasets for the same cancer. We found for a given cancer, the directions of methylation and expression changes detected from different datasets, excluding potential batch effects, were highly consistent.