A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters

摘要

BackgroundDNA methylation is essential for normal development and differentiation and plays a crucial role in the development of nearly all types of cancer. Aberrant DNA methylation patterns, including genome-wide hypomethylation and region-specific hypermethylation, are frequently observed and contribute to the malignant phenotype. A number of studies have recently identified distinct features of genomic sequences that can be used for modeling specific DNA sequences that may be susceptible to aberrant CpG methylation in both cancer and normal cells. Although it is now possible, using next generation sequencing technologies, to assess human methylomes at base resolution, no reports currently exist on modeling cell type-specific DNA methylation susceptibility. Thus, we conducted a comprehensive modeling study of cell type-specific DNA methylation susceptibility at three different resolutions: CpG dinucleotides, CpG segments, and individual gene promoter regions.