Study epigenetic changes in cancer

Methylation arrays allow researchers to quantitatively interrogate methylation across the epigenome of cancer cells at single-site resolution. Array-based methylation profiling delivers highly accurate, targeted interrogation of CpG islands, selected CHH sites, enhancers, open chromatin regions, and transcription factor binding sites.* As a high-throughput research method, arrays have a lower cost per sample compared with alternatives.

Methylation array protocols have a user-friendly, streamlined workflow with > 98% assay reproducibility and support for formalin-fixed, paraffin-embedded (FFPE) samples, increasing the applicability of methylation arrays to biobanked tissues.

*CpG: Genomic region where cytosine is directly followed by guanine; CHH: Other genomic regions where methylation can occur, defined by a cytosine that is immediately followed by any nucleotide other than guanine (H = A, T, or C)

Cancer researchers can use the assay for transposase-accessible chromatin with sequencing (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 can include genomic or transcriptomic profiling, provides insights into chromatin accessibility across the genome.

Chromatin immunoprecipitation sequencing (ChIP-Seq) is a powerful method for identifying 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 genome-wide surveys of gene regulation using ChIP-Seq.