Developing a system to simultaneously detect genetic and epigenetic information

March 11, 2021—Many diseases, most notably cancer, are associated with changes to the DNA sequence. Also altered in disease is the way that the DNA is chemically, or “epigenetically”, modified. Being able to extract genetic and epigenetic information using DNA sequencing has revolutionised biomedical research and opened new approaches to diagnosing cancer through the analysis of DNA circulating in the blood or other bodily fluids. However, no methods currently exist that can efficiently extract genetic and epigenetic information simultaneously from the same DNA sequencing data.

The most common epigenetic modification—DNA methylation—has traditionally been detected using methods that rely on a process called bisulphite conversion. But the data derived from this method is not ideal for the simultaneous extraction of genetic and epigenetic information. Recently, a new method for detecting DNA methylation, TET-assisted pyridine borane sequencing (TAPS), was developed by the laboratories of Ludwig Oxford’s Chunxiao Song and Benjamin Schuster-Böckler. It is both cheaper than bisulphite conversion and produces data of higher quality

Funded by an MRC Methodology Research Grant, Schuster-Böckler’s laboratory will collaborate with Gerton Lunter (Visiting Professor, Radcliffe Department of Medicine) to develop algorithms that simultaneously detect mutations and DNA methylation from TAPS data.  Experimental data will be provided by Song’s laboratory and those of Ludwig Oxford Director Xin Lu and Ellie Barnes of the Nuffield Department of Medicine. These test data will be used to train machine-learning algorithms to optimise the experimental parameters and accuracy of the sequencing method.

The resulting method will greatly increase the utility of the TAPS technique and could make it possible to routinely query a patient’s genetic background, while simultaneously measuring their epigenetic state. This will lead to a much broader understanding of the role of epigenetics in disease and would raise the possibility of using combined genetic and epigenetic information from sequencing data to aid earlier detection of cancer.


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