If cancer is a series of riddles hidden in our DNA, then Brisbane scientist Nic Waddell and her team at QIMR Berghofer are on the way to finding out the answers, and potentially preventing the disease in the future thanks to their world-leading cancer genomics research.
Dr Waddell and her team of researchers, working in partnership with computer scientists, analyse data from a technique called next generation sequencing (NGS). They use a complex system of computer hardware and custom-created software to analyse NGS data looking for mutations in the genomes of cancer cells, and are focused on a range of cancers including pancreatic cancer and melanoma.
In fact, earlier this year Dr Waddell co-authored an Australian-led international study that found genetic changes normally linked to colon and breast cancers could also drive a rare form of pancreatic cancer.
Published in the journal Nature, the findings mean it might be possible to identify what treatment might be of benefit to some patients and also which people are at risk of developing this cancer.
“Patients at risk of this rare pancreatic cancer could now be identifiable through genetic screening,” she said.
Dr Waddell said the study of genomics, which is done using high performance computing, would lead to more tailored or personalised treatments for patients. Melanoma is another cancer being studied by Dr Waddell through her place in the International Cancer Genome Consortium (ICGC), which is a group of researchers around the globe who are trying to characterise all the DNA mutations in thousands of cancers.
“Melanoma was recently accepted as an ICGC project and is a large project with over 500 patients and is part of the Australian Melanoma Genome Project (AMGP),” she said.
Research findings from this ongoing project found that melanomas on the hands and feet (known as acral) and internal surfaces (known as mucosal) are not caused by sun exposure, which has implications for preventing and treating them.
“We are identifying the underlying genetic landscape of tumours and we now know what is driving some tumours. Next we can use that information to look at why some people are potentially predisposed to tumours and also we can start to understand how we might treat tumours much better in the future,” she said.
“Cancer is a disease of the genome, so what happens is that a normal cell will acquire errors or mutations in the DNA of that cell and over time if those mutations hit a key part of the genome the normal cell can start growing uncontrollably or behaving incorrectly and it might lead to cancer.
“We use computer analysis to try and figure out what are the mutations or errors that exist in cancer cells and we do that because it helps us to find better ways of treating the patients.
“It tells us how the tumours develop and we may be able to find markers of early cancer so we can look to detect cancer earlier and hopefully prevent cancer in the future.”
Dr Waddell’s research group is currently studying the worst-of-the-worst cancers. The ones with the poorest outcomes like pancreatic cancer, mesothelioma, and very aggressive brain cancers.
“Forty years ago, having a diagnosis of cancer was pretty much game over, but with so many advances in research over time it means a lot of cancers now have good outcomes so my group is focused on those cancers that still have poor outcomes because if we can make a small increase in that survival then it has a huge effect for the patients.”
For now, Dr Waddell said her focus was on getting genomics into the clinic so it could directly impact treatment and become a routine part of patient care.
Just this month, QIMR Berghofer launched a company that is the first of its kind in Australia called genomiQa. It offers hospitals, clinicians and companies whole genome analysis of cancer to help tailor treatments for individual cancer diagnoses.
“Current tests being offered now might focus on just one mutation, one gene or a selection of genes, but genomiQa will focus on whole genome sequencing and we are the first Australian company to concentrate on whole genome analysis as a service,” Dr Waddell said.
genomiQa plans to offer diagnostic reports later this year to assist cancer clinicians to make more precise decisions on patient treatments within current guidelines.
“We are very focused on implementing our processes into the clinic and we are doing that with the highest quality in mind,” Dr Waddell said.
The Queensland Genomic Health Alliance (QGHA) is a five-year program focused on overcoming barriers to help facilitate the implementation of genomics into clinics and hospitals, and Dr Waddell is co-leading a group looking into the ethics, legal and social implications of genomics.
Her QGHA colleagues from QIMR Berghofer, Pathology QLD, The University of Queensland, Queensland University of Technology and the CSIRO are focused on topics including training the workforce in genomics, evaluating the impact of the research on patients, genomic testing and innovation and genomic information management.
“We are seeing very quickly that genomics is moving from research to implementation, and hopefully into routine practice in the near future. It’s an exciting time to see those impacts,” Dr Waddell said.
More targeted treatment, based on each patient’s genomic markers, is going to be one of the biggest impacts. For example, a lot of cancers have standard treatments, but thanks to the study of genomics, doctors will be better able to match the right drugs to individual patients and avoid drugs that will have no benefit.
“A lot of the chemotherapy drugs that are used have very bad side effects and are quite toxic, so to actually rule out a drug and say ‘this is not going to work for that patient’ is very useful.
Genomics also has a potential to screen DNA in patients’ blood to find early signs of tumour formation. In the future, Dr Waddell predicts that genome sequencing will also focus on how to treat the populations of cells in tumours called clones that can become resistant to drugs.
For Dr Waddell, Brisbane is the perfect place to live, work and play.
“I arrived to Australia from the UK in 2003 and I think the city is amazing – it’s green, it’s vibrant, there are a lot of outdoor things to do and the science industry has taken off over the last 10 to 15 years,” she said.
“We’ve got some amazing facilities like QIMR Berghofer, University of Queensland, Queensland University of Technology and the Translational Research Institute. All really top-class institutes around town.”