A new software tool able to detect a short genetic add-on related to cancer could lead to quicker diagnosis of the disease.
Developed by a team of researchers from Johns Hopkins University, the Ontario Institute for Cancer Research, and the University of Toronto, the software detects the presence of a type of epigenetic addition to DNA called cytosine methylation.
Cytosine is one of the four main building blocks of DNA. Cytosine methylation refers to the presence of an extra attachment to cytosine blocks. This addition can determine whether vital genes are switched on or not and therefore whether cells operate correctly.
High levels of cytosine methylation have been linked to the development of several diseases, including cancer.
Current methods to measure cytosine methylation of DNA samples can be a particularly difficult process due to the fragility of samples and the demand to use large amounts of pre-treated tissue samples.
The team’s software solution works with a commercially available nanopore sequencing device called the MinION sequencer, itself the size of an average USB stick. resulting in an accessible tool that measures DNA methylation of small samples.
The sequencer is dotted with 512 minuscule holes through which DNA is fed whilst an electric current is applied. Changes in the electrical current identify the DNA sequence and, with the addition of the new software, can now identify DNA methylation.
Researchers initially ‘trained’ their software using synthetic DNA in order for it to learn to distinguish between methylated cytosine and normal cytosine. The software was then tested using human breast cancer cell DNA, for which researchers found their solution to be successful in detecting methylation.
Reza Moridi, Ontario’s minister of research, innovation and science, commented on the findings: “These new insights into DNA methylation could help lead to new and innovative ways to detect and treat cancer.”