Epigenomic profiling at genome scale: from assays and analysis to clinical insights

Recent years have seen a massive decrease in the cost of sequencing technologies which has had a profound effect on the quantity and range of epigenomic data available to cancer researchers. In this chapter, we provide a brief overview of some of the key technologies used to generate this data, including approaches to assay DNA methylation, histone modifications and alternative histones, three-dimensional chromatin architecture and accessibility, and small/noncoding RNAs. We discuss new single-cell approaches, which are essential to understanding the role of epigenomic heterogeneity in tumorigenesis, tumor progression, metastasis, and response to treatment. We also describe some of the primary international consortia and epigenomic data resources available to researchers. Finally, we provide an overview of some common analytical approaches and tools for different types of epigenomic data and present two case studies detailing the integration of epigenomic and other data to provide clinically relevant insights.