New Gene Sequencing Software Could Aid in Early Detection and Treatment of Cancer

Winston Timp, an assistant professor of biomedical engineering, supervised research on new computational software that determines if a human DNA sample includes an epigenetic add-on linked to cancer and other health conditions.

Timp, along with research technologist Rachael Workman, and team members from the Ontario Institute for Cancer Research, and the University of Toronto provided details on this new method in the Feb. 20 issue of the journal Nature Methods. This technique detects the presence of an extra mark on DNA called cytosine methylation.

Cytosine is one of the four main genetic building blocks, or nucleotides, that make up DNA. Methylation simply refers to the presence of a biochemical (methyl) group attached to a nucleotide, in this case cytosine. This altered version of C can affect the way important genes are switched on or off. Such genetic miscues can play havoc with healthy activity within cells.

“This technique can read long pieces of DNA and see changes in the extent of methylation in the sample,” said Timp. “It let us look at how the changes in methylation appear on individual molecules as they pass through this pore.”

In order to help advance this research, the team members have made their nanopore sequencing software for detecting DNA methylation available on an open-source basis at https://github.com/jts/nanopolish.

“We’ve taken this line of research a critical step further ahead,” Timp said. “My hope is that others in this field will begin using the software right away.”

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