Some say the bigger the better, while others believe it’s what you do with it that counts! Now, a study reports that the most recent iteration of EPIC DNA methylation (900K EPIC v2) microarrays – which supercharges your insight by taking in both many more informative CpGs and additional chromatin features – supports the efficient high-throughput profiling of the human DNA methylome.
The 900K EPIC v2 microarray from Illumina covers ~935,000 CpG sites and targets additional DNA cis-regulatory elements (e.g., enhancers, super-enhancers, and CTCF-binding regions) and open chromatin regions identified via ATAC-Seq/ChIP-seq. DNA methylation-mad researchers led by Manel Esteller (Josep Carreras Leukaemia Research Institute, Barcelona) were keen to try out the 900K EPIC v2 microarray and technically and biologically validate its ability to support user-friendly research into how epigenetics impact physiological and disease-associated mechanisms.
Let’s hear from Noguera-Castells and colleagues on how to supercharge your DNA methylation analysis:
- After detailing the improvements in comparison with previous iterations, the authors technically evaluate the 900K EPIC v2 microarray (936,866 CpG probes) by hybridizing:
- a lung tumor sample and comparing results with those from the previous EPIC (850K) microarray, finding a close correlation between the methylation levels detected at each CpG site for shared probesthe same breast cancer and blood samples twice in different 900K EPIC v2 microarray chips, reporting the highly correlated nature of methylation values derived from each experiment
- two normal human endometrium samples obtained from consecutive fresh or formalin-fixed paraffin-embedded sections, demonstrating the close correlation of results from fresh and frozen samples at each CpG
- Next, the team biologically evaluate the 900K EPIC v2 microarray by:
- comparing DNA methylation profiles of forty-three samples (normal and tumor tissues and cancer cell lines) to the previous 850K microarray, which demonstrates the improved robustness of the new iteration
- performing unsupervised hierarchical analyses of normal and tumor tissue from lung and blood from the above experiment, which permits the easy discrimination of healthy and tumor samples for both tissues
These epigenetically-enthusiastic authors provide evidence for the biological reproducibility and feasibility of the bigger, better-equipped 900K EPIC v2 methylation microarray and confirm a significant improvement on the EPIC (850K) predecessor. Overall, this technological advance covers many more CpGs, easily distinguishes normal and tumor samples, and represents a handy tool for the further interrogation of the cis-regulatory regions of the human genome.
For more on how the 900K EPIC v2 methylation microarray can supercharge your DNA methylation analysis, see Epigenetics, March 2023.