A novel machine learning framework for phenotype prediction based on genome-wide DNA methylation data

DNA methylation (DNAm) is an epigenetic mechanism used by cells to control gene expression, and identification of DNAm biomarkers can assist in early diagnosis of cancer. Identification of these biomarkers can be done using CpG (Cytosine-phosphate guanine) sites, or particular regions in DNA. Previous machine learning methods known as MS-SPCA and EVORA have been used to link DNAm biomarkers to specific stages of cervical cancer using CpG data. In this paper, we propose a novel machine learning framework that yields greater AUC accuracy than the MS-SPCA and EVORA for predicting stages of cervical cancer using CpG data. This framework appears to be promising in regards to the data examined herein as well as for future biological studies.