Written By
Bianca de Loryn
College/Division
College of Healthcare Sciences
Publish Date
10 November 2023
Related Study Areas
Focusing on Bioinformatics
JCU PhD candidate Rhys Gillman believes that more lives can be saved if doctors can personalise cancer treatments. Rhys wants to help by finding the best combination of cutting-edge cancer analysis algorithms which will help doctors choose the most effective chemotherapy treatment for each patient.
Rhys specialises in Bioinformatics, which is a major within the Biomedical Sciences field. This means that for Rhys, the most important tool in the lab is not the Petri dish or the microscope but the computer. “Working in bioinformatics essentially means working with biological information, but from the mindset of programming and working with really large data sets,” he says.
“Over the past decade or so, scientists have been getting better and better at sequencing human DNA and RNA,” Rhys says. DNA carries the instructions for building every aspect of the body, and RNA is the intermediate messenger that can tell us which parts of our DNA are active or inactive. Cancer arises due to acquired mutations in our DNA which can either switch off genes or make them overactive, which can be detected in the RNA levels.
“Having access to this large amount of sequenced data from a single patient allows us to develop more individualised cancer treatments, but also requires us to incorporate more computer programming and data science into biology,” he says.
This has not always been the case, Rhys says. “A lot of previous approaches to cancer treatment have tried to find one chemotherapy to treat all individuals with a specific type of cancer. The problem is that the cancer in each patient can be caused by different mutations, and this means that different treatments are needed for each patient.”
But having access to the DNA data of an individual tumour can help, Rhys says. “The aim of my PhD research is to match the best drug with each individual patient based on the DNA sequence of their tumour.”
Researching liver cancer
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 Lionel Hebbard, 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 algorithms 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 comparing six algorithms 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.
Working with patient samples
As soon as Rhys has refined the process for the algorithms, he is planning to use DNA samples taken from real liver cancer patients instead of the publicly available datasets he is currently using.
“We're collaborating with a surgeon at the Townsville University Hospital to gain access to samples where they have removed the tumour as well as a small amount of healthy liver surrounding the tumour," Rhys says.
“I will take that back to the lab, sequence the DNA of the tumour and the healthy tissue and then work from there.” Rhys says he will also be using liver cancer cell lines that are commercially available. “They're used as a standard by everyone in the world,” he says.
Once he is finished with his research in late 2024, Rhys expects that future medical scientists will be able to run a combination of algorithms based on his research findings. The results can then be used to find the best available personalised chemotherapy treatments for every individual patient with different types of cancers. Rhys is hoping that his research will improve the effectiveness of the treatments that patients are given and ultimately, save lives.
Rhys has also recently won a 3 Minute Thesis (3MT) competition where he described in a video how personalised cancer treatments work in easy-to-understand terms.
Working in biomed is challenging and rewarding
Rhys had originally aimed at becoming a medical doctor, but he is happy now that he decided to study a Bachelor of Biomedical Sciences, majoring in Molecular and Cell Biology. “I enjoy working in biomed research. Everything's worked out for me,” he says.
He adds that the best thing about working in this field is that every day there are new surprises. “Just every day doing something that other people haven't done before in research, that's what keeps me going,” he says. “That often means that there's a new problem every day and a new hurdle to get past and work out. But that is what keeps it interesting.”
Want to learn more about research at JCU?
Rhys’ PhD advisor, Associate Professor Lionel Hebbard, is currently looking for Honours, Master’s and PhD students who are interested in researching the following topics: “Understanding new regulators of liver cancer progression” and “the role of novel genes in muscle growth”.