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Genomic Cancer Medicine Program

Using genomics to improve the understanding, early detection, prevention and management of cancer.

Genomic medicine is the future for all cancer treatment, but has the greatest impact on rare, high-mortality cancers which are more difficult to diagnose and treat. The Australian Genomic Cancer Medicine Program (AGCMP) focuses on improving health outcomes for patients with less common, high-mortality cancers, including ovarian, and pancreatic cancer, sarcomas and cancer metastasis.

While rare cancers are individually less common, they collectively account for around a third of cancer incidence and nearly half of cancer deaths in Australia. 

Genomic medicine offers an innovative strategy for diagnosing and treating cancer, based on a person’s entire DNA sequence. Variants in the DNA sequence determine the differences between individuals, and between types of cells (e.g. tumour cells and non-tumour cells). We use the latest genome sequencing technologies to look at the genetics of the cancer, rather than treating it based on location (e.g. breast, colon, skin). This allows us to understand inherited cancer risk and find more effective treatments for people with cancer. 

The Genomic Cancer Medicine Program is an innovative suite of clinical trials and studies that matches therapies with individuals on the basis of genomic information.

1Clinical trials

Run clinical trials to identify more effective therapies for rare and less common cancers. 

2Cancer genetics

Study heritable cancer risk and risk management, to mitigate the development of disease.

Our partners

The Genomic Cancer Medicine Program (GCMP) was established as part of a $24 million, four-year investment by the NSW State Government in using genetic technologies to improve patient outcomes. We collaborate with clinicians, pharmaceutical companies and funding partners who share our vision. 

  • St Vincent’s Hospital Sydney 
  • NSW State Government
  • NHMRC Clinical Trials Centre (University of Sydney) 
  • AstraZeneca
  • Pfizer 
  • Roche 
  • Vodafone Foundation
  • Rare Cancers Australia 

Australian Genomic Cancer Medicine Program

More than 162,000 Australians are diagnosed with cancer every year. About 52,000 of these patients will be diagnosed with a rare or less common cancer.

Cancer is usually considered a disease of older people, with mortality rates increasing with age for most cancers. One of the key characteristics of rare cancers, however, is that these cancers place a great burden on children and young families. In every age group, ‘rare’, high-mortality cancers are the most common cause of disease-related death in Australia. Together with less common cancers, they account for over half of all cancer deaths.

Reasons for these high mortality rates include:

  • Difficulty in diagnosis (as they are seen less often)
  • Standard treatments are often less effective
  • Limited access to new therapies.

While there's excellent evidence that participation in standard clinical trials is associated with better outcomes for people with cancer, patients with rare or less common cancers have very limited access to them. Despite there being over 180 types of rare cancers, trials are often not financially feasible to run for the small numbers of patients with these diseases.

Our programs

The Genomic Cancer Medicine Program uses Garvan’s whole-genome sequencing facilities in the MoST Clinical Trials to identify more effective treatments for cancer patients, and to understand heritable cancer risk in the Genetic Cancer Risk in the Young (RisC) study and risk management as part of the Surveillance in the Multi-Organ Cancer prone syndromes (SMOC+) Study.

Genome sequencing helps clinicians diagnose illness and provide better, more personalised treatment.

Genomic information can predict how a person’s cancer will respond to surgery or drug therapy, guiding the use of existing treatments, or suggesting more targeted treatments. This can spare some patients costly and complex procedures, and can result in better outcomes.

Genomic information also helps us understand the genetic drivers that increase a person’s risk of developing cancer. Identifying that a patient is at risk allows personalised monitoring and more effective early detection.

Targeted therapies

We have developed targeted approaches to treating rare and less common cancers, using two specific strategies:

  • Drugs which inhibit tumour growth  
  • Immunotherapies which stimulate an immune response that delivers long-lived tumour destruction. 

These medicines, which work on differing cancer mechanisms, offer patients a more individualised approach to cancer treatment. 

We're also working to understand more about the heritable causes of cancer and risk management, and are developing new diagnostic techniques and treatments to improve the health outcomes of individual patients, and all Australians.

The GCMP runs clinical trials to identify new treatments for patients with rare or less common cancers. If you're interested in participating in trials, please read the information below.

For questions about the program, please email: 

Our staff will get back to you as soon as possible, however please allow a day or two for us to process your request.

The MoST clinical trials 

The Molecular Screening and Therapeutics (MoST) clinical trials personalise experimental treatments based on an individual’s unique cancer genetic profile. Because of this, eligibility for participation is independent of where the cancer arises in the body. In these trials, rather than focusing on a tumour’s location, such as the ovaries or pancreas, patients who have a shared harmful genetic variant, are treated with a drug that may target the variant, even if they have different types of cancer.

Clinical trials are generally used to test a new treatment, with some patients getting the new drug and the others getting an existing drug or a placebo. One-third of GCMP patients will have a biomarker matched to a targeted therapy, while those remaining may be directed on to other trials or therapies, including immunotherapies.

The clinical trial process 

Traditionally, clinical trials for new drugs have been conducted in four to five phases, taking around eight to 10 years to complete. The financial costs of conducting cancer clinical trials have risen from less than US$10,000 per patient in 1980, to around US$47,000 in 2011.

Because there are fewer patients with rare cancers, it isn’t possible to follow the usual progression of clinical trials mechanisms for these small groups of patients.

While phase 1, 2 and 3 studies are, – and will remain, – critical to drug development, they are costly and slow. New trial designs, such as MoST, which sit between a phase 1 toxicity trial and a phase 2 efficacy trial and include genetic testing of cancers, offer opportunities for trialling targeted treatments more efficiently. MoST has already shown that genomic cancer profiling can identify treatable options for a significant portion of patients who previously had none.

Joining the MoST clinical trial 

Our trials seek to determine if a treatment will work, or work more effectively than another treatment. First, all patients (and their tumours, where possible) are genomically screened to see if they're suitable for the trial and if there are variants that can guide treatments.

After screening, patients are offered either:

  • MoST clinical trials, including immunotherapies
  • Clinical trials outside MoST that use molecular eligibility criteria
  • Other biomarker-guided treatments outside MoST

All participants, including those with no ‘actionable’ biomarkers are informed of the results of the screening through their own doctors.

Joining the immunotherapy trials 

The MoST protocol is also conducting clinical studies to test new immunotherapy drugs in patients with high-mortality cancers. The first MoST immunotherapy sub-study tests a combination of so-called ‘immune checkpoint inhibitor’ drugs that take the brakes off the anti-tumour immune response, enabling immune cells to attack cancer cells. A second immunotherapy study, for patients with specific genetic abnormalities in their tumour, combines a targeted treatment with a checkpoint inhibitor.

Although immunotherapies are proving to be effective in many cancer types, they do not work in all patients. We're seeking biomarkers that can predict which patients will benefit from specific treatments targeting the immune system, and to better understand how immunotherapies work to fight cancer. With this knowledge, we aim to develop a more precise approach that tailors immunotherapy treatment to individual patients, based on the characteristics of their immune system and its interactions with tumour cells.

The immunotherapy trials will allow us to understand how these immune biomarkers influence the anti-tumour response, and help develop a precision approach where treatment can be personalised.


All component studies of the Genomic Cancer Medicine Program have been approved by the St Vincent’s Hospital Sydney Human Research Ethics Committee, which operates under the requirements of the National Health and Medical Research Council’s National Statement on Ethical Conduct in Human Research (2007), the Australian Code for the Responsible Conduct of Research (2007), and for research specific to NSW, the NSW Supplement to the National Statement (2008). 

Patient stories

  • Paul and Wendy Jeans’ daughter Cathie was a vibrant, fit and busy wife and mother of three teenage boys. She was approaching her 49th birthday when she was diagnosed with gall bladder cancer at the end of 2014.

    Paul: Cathie had had occasional abdominal pain and bloating and some gastric reflux, which was thought perhaps to have been gall bladder-related, though not sufficiently worrying to her GP to have any tests done.

    Our family has always been very close and Wendy and I have been deeply involved in Cathie and her husband Joe’s life, holidaying together, looking after the boys. Cathie’s diagnosis of gall bladder cancer and prognosis of only six months was just devastating.

    Cathie was typically stoic and, as her diagnosis was somewhat inconclusive, we optimistically hoped that the tumour might have been a secondary metastasis from a potentially more treatable primary colon cancer.

    Indeed, Cathie was initially treated with chemotherapy drugs for colon cancer, but after a number of failed courses and the deterioration of her liver function, Cathie underwent a major operation to install stents and bypass part of her bowel in March 2015. She also underwent a course of chemotherapy drugs for gall bladder cancer, but this treatment did not produce any improvement either.

    Through my association with University of Newcastle and the Hunter Medical Research Institute, it was suggested that we have Cathie’s genome mapped to find chemotherapy drugs that may be effective in her particular case. This analysis confirmed that her current chemotherapy drugs would be unlikely to work, but it also suggested that two other drugs, not normally used with gall bladder cancer, may have potential.

    After three cycles of treatment, this third combination of chemotherapy drugs resulted in an 80% reduction in Cathie’s cancer markers, but by then it was too late to save Cathie. She died at the end of August 2015.

    Cathie’s brave fight had totally exhausted her, and the complexity and seriousness of her situation meant that she spent most of her last six months in hospital, rather than with her family. The impact of not only losing one’s child, but seeing her devastated physically and wracked with pain is the most painful experience a parent can have. You continue living, but it is in a world that is very different from the one you enjoyed with your child. Cathie’s husband, Joe, and three boys miss her enormously, and Cathie’s sister and brother also continue to be deeply affected.

    We now know that some rare cancers are extremely difficult to diagnose and many GPs are not equipped to do so. We also know that personalised treatment, determined through genetic analysis, is essential and it is possible that drugs designed for one purpose may work in another situation.

    We need to try and determine people who may have a particular predisposition to rare cancers. We have experienced other cancers in our family, but none have been terminal. Our wider group of friends have not all been so fortunate. The public needs to be more aware of rare cancers and their significance to the Australian community.

    The 'soft' side of patient care is also extremely important in situations like Cathie’s. Some of her doctors lacked the necessary interpersonal skills and that, in itself, negatively impacted her condition.

    Meeting Professor David Thomas at Garvan convinced us of the value of his ideas. Apart from his particular goals, his approach to the experimental model (large steps rather than incremental change requiring expensive and time-consuming trials) has real potential to change the way we go about medical research.

    As a family, we are targeted philanthropists, we give to causes about which we are passionate. Remembering Cathie is of the utmost importance to us and we feel we can do that most effectively through supporting Professor Thomas’s work at Garvan, and thereby making a real difference to others who may find themselves in her situation.

  • In 2012, doting 59-year-old grandad, Darin Mallawarachchi, was at home carrying his grandson when he slipped on the staircase and hit his tailbone. The ensuing scan revealed a 3cm chordoma tumour – a rare type of bone cancer – on his sacrum, the triangular bone just above the bottom tip of the spine. Darin was very active and in good health, going to the gym regularly.

    "Although I was lucky that the tumour was detected very early, it was still such a shock. We are a very close family – I have three grown-up daughters, and three grandchildren with another on the way. My whole family was very worried, and stressed," said Darin.

    Following successful surgery in September 2012 to remove the tumour, it took Darin, six long months to recover from postoperative complications.

    An MRI scan in December 2013, detected a new 2cm tumour. This was treated with stereotactic radiation in March 2014, but unfortunately the tumour continued to grow. As a result, in March 2015, Darin underwent radio frequency ablation treatment, instead of surgery, to remove the tumour as far as possible. As the tumour was almost touching a nerve, saving the nerve meant not eradicating the whole tumour.

    "Follow-up scans, in October 2016, showed the residual tumour had increased in size, and in November 2016, I was treated with radio and microwave ablation therapy. I would like to thank the doctors and surgeons who provided me with an excellent standard of care.

    Now I have pains and aches at the base of my spine and right leg, which is also now weaker. All the procedures which I underwent, have left me with bladder and bowel problems. In early 2017, I was enrolled into the MoST immunotherapy clinical trials program at Garvan, following an introduction by Rare Cancers Australia. Hopefully, the immunotherapy treatment can destroy the residual cancer cells, which are at the base of the nerve.

    It is true that life is different now and I am not quite the same person as before; however, life continues to hold much happiness, and hope. I am able to keep positive. I have grown stronger and more determined to take each day as it comes and beat this cancer.

    Garvan is providing pioneering research and clinical trials treatment to cancer patients in Australia, but the availability of the clinical trials isn’t widely known. It’s vital that more patients have access to rare cancer drug trial programs.

    I am excited knowing that Garvan has made remarkable strides towards new treatments that will mean better outcomes for everyone affected by this rare disease. I hope that supporting and being part of Garvan’s research will help find a drug or medical solution in the future for those who are diagnosed with rare cancers," he said.

    By August 2017, after six months on the trial, Darin’s cancer is responding to therapy and there is evidence that the tumour is shrinking.

  • Zara D’Cotta was diagnosed with breast cancer nine days before her 30th birthday. Two years later, she was diagnosed with a melanoma on the morning of her breast cancer anniversary.

    "I’d been for a walk along the St Kilda foreshore at sunrise to commemorate it and reflect on how far I had come. It finally all seemed like a distant memory, but life can change so quickly. I spent my second birthday in three years recovering from surgery, waiting to find out if my cancer had spread," Zara said.

    Zara had a lumpectomy for her localised breast cancer, but then went on to have six weeks of daily radiotherapy to minimise the risk of recurrence.

    "It felt completely bizarre as a fit, healthy young woman, to leave my corporate job every day to sit in a white hospital gown, surrounded by people much older than me, waiting to be zapped by a machine so big it looked like it belonged on a space ship. While there were no visible signs of the side effects, it was physically exhausting and mentally challenging."

    Zara then started the anti-hormone medication, tamoxifen. "My side effects were so severe I had to stop working. Just putting one foot in front of the other felt like a huge task. At its worst, I felt hazy and couldn’t do basic things like drive my car. I’d burst into tears for no real reason. After 15 months, I stopped taking tamoxifen because of the degree to which it was affecting my quality of life. Thankfully, my melanoma also hadn’t spread to any nerve or blood cells. I had surgery to remove all the surrounding tissue and didn’t require any further treatment.

    It was an extremely difficult time for us all. I don’t think I’ll truly appreciate or understand what it must have been like for my mother until I have children myself, but I know that as a parent you want to do whatever you can to protect your child. To be in a situation like that and not be able to do anything, and also have to stay strong for your child, must have been awful and terrifying. It was when I received the call from my surgeon to say that my breast cancer hadn’t spread and my mum burst into tears with relief that I realised how worried she had been.

    My mum was diagnosed with breast cancer one month after my breast cancer diagnosis. It was a different type of cancer to mine, and I tested negative for the BRCA gene mutation, so we are not sure whether they are genetically linked.

    I consider myself very lucky to be cancer free, but the cancer treatments and stress from the two cancer diagnoses have taken their toll. I have learned so much because of this experience though and the knowledge I have gained, and continue to gain on this journey, is hugely empowering.

    I am really excited to be part of the Genetic Cancer Risk in the Young study. When I was first diagnosed with cancer four years ago, I was prepared to accept that I may never know why I got cancer. To think that I may soon know the reasons is absolutely mind-boggling. I am in awe of the work of the wonderful team of researchers at Garvan – the discoveries they have made fill me with great hope that we will see a cure for cancer in my lifetime."