New tool pinpoints genetic sources of disease

Many diseases are the result of either variations in the genome or reversible chemical changes to DNA, known as the epigenome. New data obtained by Johns Hopkins scientists show a connection between genetic variants and epigenetic information. These findings could help discern clues regarding the causes and possible treatment of complex genetic conditions, including many cancers and metabolic disorders.

Chmistry of Life

The genomes of healthy and sick populations are commonly compared in order to identify predispositions for diseases, but until now it has not been possible to compare epigenomes. Professor Andrew Feinberg explained that it has long been known that individual genetic variants in sections of DNA that don’t contain blueprints for proteins seem to alter the quantity of proteins produced far afield. That phenomenon has made it very hard for researchers to pinpoint the source of some genetic diseases or targets for their treatment. Feinberg says “Epigenetic tags show how disease-causing genetic variants might affect distant genes that in turn contribute to the disease."

Professor Feinberg's team first analyzed genetic data from hundreds of healthy participants in three studies to determine what a normal epigenetic pattern looks like. Epigenetic signatures were found to occur in blocks, in the same way as genetic code. They then focussed on one type of epigenetic change, the attachment of a methyl group to a particular site on DNA, which the team dubbed “GeMes,” for methylation blocks controlled by genes. Finally, they investigated the relationship between the resulting epigenetic data and genetic data.

The researchers found that the GeMes overlapped with the long genetic blocks but were much shorter. This led them to suspect that the protein-coding genes turned on or off by those tags must be at the root of the disease associated with a particular genetic variant found elsewhere in the block.  Yun Liu, a postdoctoral fellow in Feinberg’s laboratory commented that “Previously, people could not pinpoint the variants within a long stretch of DNA that were responsible for the disease, but now, by detecting just one variation in DNA methylation, or one GeMe, a researcher will know that one or more of the few hundred methylated nucleotides are possibly causing the disease.”

Feinberg says he hopes these findings will encourage the inclusion of epigenetic analyses in ongoing genetic analyses of disease. His group’s next step will be to look for GeMes associated with specific diseases, such as Crohn’s disease and cirrhosis.


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