High-throughput genomic array accelerates DNA methylation analysis

BioTechniques News
Beatrice Bowlby

As mice are a vital model organism and DNA methylation is commonly used in epigenetic studies, researchers have developed a high-throughput genomic array for DNA methylation for a more detailed view of the mouse epigenome.

Since the 1980s, the role of epigenetics in diseases like cancer, which we now understand to be driven by both epigenetic and genetic mutations, has become increasingly apparent. A paper published in Cell Genomics reports a new genomic array to study the role of methylation in both healthy processes and in diseases like cancer in more depth. Researchers at the Van Andel Institute (MI, USA) and the University of Pennsylvania (PA, USA) collaborated with industry partners Illumina (CA, USA) and FOXO Technologies (MN, USA) to create this new tool.

This new genomic array contains more than 296,000 probes, representing the diversity of DNA methylation biology in mice and related rodents. The array includes markers for many biological features such as genomic imprinting, aging, cancer and germ cell development.

“We learned many lessons from the current and previous generations of human arrays and have improved the overall quality of probe design,” said Wanding Zhou (University of Pennsylvania), the first author of the study. “For example, we optimized the probe selection to cover the diverse biology of DNA methylation in mice while minimizing the chance of probe misuse and artifacts.” The array also contains probe sets to enable comparative analyses between human and mice genomes, as well as among other rodents. In comparison to previous methods, this array allows scientists to study methylation more quickly and in greater detail.

Computer model identifies cancerous driver mutations

Researchers have developed a computer model to scan the entire genome of cancer cells to identify driver mutations, which could help researchers find novel drug targets.

The research group used this high-throughput genomic array to develop an atlas of DNA methylation profiles across more than 1200 samples that included a range of cell types, strains and pathologies. While DNA methylation data was previously available, it was not centralized; this DNA methylation atlas centralizes the data.

The researchers repeated experiments from earlier epigenetics research to validate the array, finding that it corroborated with the original results and did so much faster.

Peter Jones (Van Andel Institute), one of the co-authors, concluded: “It allowed us to further validate work we did more than 40 years ago. Its speed, depth and efficiency will allow us to accelerate discovery by identifying genetic and epigenetic changes more quickly and in greater detail than ever before.”

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