Rhys’s PhD research is specifically focusing on developing treatments for liver cancer. “Liver cancer has one of the most rapidly increasing mortality rates in Australia,” he says, adding that some of the leading causes of liver cancer include alcohol, tobacco, diabetes or obesity.
“I work in a group with Associate Professor , whose research focuses on liver cancer,” Rhys says. “There are not many effective ways of treating liver cancer at the moment other than surgery, which only works if the cancer is detected early enough. We don't really have any effective drugs to treat it.”
Even though Rhys’s research focuses on liver cancers, Rhys wants people affected by other cancers to benefit from his research as well. “This is why I will be trying to apply my research as broadly as I can,” he says.
Comparing cutting-edge algorithms
Bioinformatics is a relatively new area of research, and the that Rhys is working with have only been developed over the last decade. An algorithm is a set of instructions that a computer carries out in order to solve a certain problem.
For his PhD, Rhys is to identify which ones perform best when it comes to identifying the correct ‘drivers’ of cancer. Drivers are the DNA mutations that are actually responsible for driving growth of the tumour. Rhys says that so far it has been difficult to say how effective the algorithms are as they have all been tested with different datasets.
“A lot of my work has been in making adjustments to the code of these algorithms. I want to make sure that everything will run with the exact same input data,” Rhys says. “I want to be able to compare apples with apples and have everything on a level playing field.”
Patience is key when testing algorithms
For now, Rhys takes publicly available datasets from cancer cell lines grown in a lab, and runs them through his six algorithms. He then compares the results from the six algorithms to determine which one is most effective at identifying a specific cancer cell’s drivers. This will then allow doctors or oncologists to determine how the cancer should be treated.
As of late 2023, Rhys is focusing on trialling his selection of algorithms. “I've got something running at the moment that has already taken about three days. It's looking like it's probably going to take about a week before I have my results,” he says.
Some of the test runs are being conducted at JCU’s High Performance Research Computing (HPRC) system which is run by JCU’s eResearch Centre in Townsville. Rhys says he needs high performance computers to work on this because his six algorithms are analysing thousands of genes in over 1,200 samples, and all at the same time. This takes a lot of time.
“Once we have worked out which is the best approach, this analysis should be able to run on a regular office computer, though, which is important for this technology to be used clinically,” Rhys says.