Cancer is a disease of the genome, but genetic mutations are only one factor. Non-genetic changes also affect the phenotype. Understanding the epigenetic landscape is increasingly crucial for modeling cancer initiation, progression, and therapeutic responses. Epigenomics looks at how cells control gene activity through processes such as DNA methylation.
Epigenomic technologies can identify cellular biomarkers associated with regulation of cancer genes or drug resistance:
Cancer researchers can use ATAC-Seq to study epigenetic features across the genome without prior knowledge of regulatory elements. ATAC-Seq exposes genomic DNA to Tn5, a highly active transposase that preferentially inserts into open chromatin sites and adds sequencing primers. Subsequent NGS analysis, which includes genomic or transcriptomic profiling, provides insights into chromatin accessibility across the genome.
While several traditional methods like chromatin immunoprecipitation sequencing (ChIP-Seq), formaldehyde-assisted isolation of regulatory elements sequencing (FAIRE-Seq), or DNase I hypersensitive sites sequencing (DNase-Seq) can be used to study regions of chromatin–DNA interaction sites, ATAC-Seq illuminates regions of open chromatin.
Methylation arrays allow researchers to quantitatively interrogate methylation sites across the epigenome of cancer cells at single-nucleotide resolution. Array-based solutions provide comprehensive genome-wide coverage that includes but is not limited to CpG islands, CHH sites, enhancers, open chromatin, and transcription factor binding sites. As a high-throughput research method, the cost is minimal per sample compared with methylation sequencing alternatives.
Methylation array protocols have a user-friendly, streamlined workflow with >98% assay reproducibility and support for FFPE samples, increasing the applicability of methylation arrays to biobanked tissues.
Learn more about methylation arrays
Chromatin immunoprecipitation (ChIP) assays with sequencing (ChIP-Seq) is a powerful method to identify genome-wide DNA binding sites for transcription factors and other proteins. This method can reveal insights into gene regulatory events and biological pathways that play important roles in the development and progression of some cancers. Illumina offers efficient workflow solutions to enable you to perform genome-wide surveys of gene regulation using ChIP-Seq.
An overview of Illumina sequencing followed by workflow suggestions for popular cancer research methods.
This guide provides multiomic research examples from recent literature along with detailed, end-to-end workflows. See recommendations for sample isolation, library prep, sequencing depth, data analysis, and more.
This infographic serves as a visual guide to see why epigenomics greatly impacts the understanding of cancer.
Cancer biology experts discuss the many advantages of leveraging methylation microarrays for biomedical research.
Learn how to link the causes and consequences of complex phenotypes through multiomics to enable discoveries that weren’t possible before.