  The research reported in this paper identifies the epigenetic biomarker
(methylation beta pattern) of breast cancer. Many cancers are triggered by
abnormal gene expression levels caused by aberrant methylation of CpG sites in
the DNA. In order to develop early diagnostics of cancer-causing methylations
and to develop a treatment, it is necessary to identify a few dozen key
cancer-related CpG methylation sites out of the millions of locations in the
DNA. This research used public TCGA dataset to train a TensorFlow machine
learning model to classify breast cancer versus non-breast-cancer tissue
samples, based on over 300,000 methylation beta values in each sample. L1
regularization was applied to identify the CpG methylation sites most important
for accurate classification. It was hypothesized that CpG sites with the
highest learned model weights correspond to DNA locations most relevant to
breast cancer. A reduced model trained on methylation betas of just the 25 CpG
sites having the highest weights in the full model (trained on methylation
betas at over 300,000 CpG sites) has achieved over 94% accuracy on evaluation
data, confirming that the identified 25 CpG sites are indeed a biomarker of
breast cancer.
