The Medical Genomics Team analyses next generation sequence data to address clinical challenges in a variety of diseases. The approaches we take include:
Ultimately, we aim to take steps towards ‘personalised medicine’ to enable the diagnosis, management and treatment of patients.
Since 2017, we have been part of the Queensland Genomics program exploring the Ethical, Legal and Social Implications (ELSI) of genomics within Queensland’s health system. Queensland Genomics is a Queensland Health initiative that seeks to accelerate the adoption of genomic medicine into mainstream healthcare to benefit all Queenslanders. In addition to her research work, Dr Waddell is an active advocate for patient perspective in genomic research. She is a member of the Queensland Genomics Community Group which advocates for the patient voice in medical genomics across Queensland.
In partnership with Queensland Genomics Dr Waddell and her team explore a variety of areas including:
The Medical Genomics team works on a variety of tumour types gain a better understanding of disease biology, drug responses and to identify novel therapeutic strategies. Using whole-genome (long and short read), RNA sequencing and methylation technologies allows us to study disease heterogeneity and identify genomic signatures that can be used as biomarkers of treatment response.
The tumours which we study include melanoma, oesophageal cancer, breast cancer, ovarian cancer, mesothelioma and lung cancer. Our work is in collaboration with a variety of partners and some example of our work include:
Australia has one of the highest rates of melanoma in the world. Melanoma is a type of skin cancer usually caused by overexposure to the sun. Rarer forms of melanoma can also occur on body sites without sun exposure, such the inside of the eye (uveal), on the soles of the feet (acral) and internally on mucous membranes such as inside the mouth (mucosal melanoma).
The Medical Genomics laboratory is part of the Australian Melanoma Genome Project, which involves more than 50 researchers from Melanoma Institute Australia, The University of Sydney, Royal Prince Alfred Hospital, Westmead Institute for Medical Research and QIMR Berghofer Medical Research Institute (involving the Medical Genomics, Genome Informatics and Oncogenomics groups). In this project, we are using whole genome sequencing technologies to identify common genetic mutations in melanoma tumours from more than 500 patients. It is hoped that discovering such information will help doctors to better personalise the treatment of melanoma.
Lung cancer is a common disease and many patients have a poor survival. We are studying the genomics of lung cancer to identify therapeutic targets including those that are associated with immunotherapy response. We are part of a large national lung cancer project led by the Royal Brisbane and Women’s Hospital (RBWH) that is recruiting patients for whole genome and RNA sequencing. This project aims to improve diagnoses of cancers and determine why some patients respond well to immunotherapy while others do not.
Part of our research focuses on the study of gynaecological cancers, including ovarian and endometrial cancers. This is done through comprehensive genomic analysis of pre-clinical models as well as public data.
Diagnosing Inherited Disease
We use whole genome sequencing to identify germline events which may be contributing to disease.
The Medical Genomics team is currently analysing sequence data within the Hereditary Cancer Syndromes ICCon (Inherited Cancer Connect) project. The ICCon partnership is a Cancer Council NSW-funded national collaboration of Familial Cancer Centres. It aims to identify genetic variants in the normal DNA of patients with a suspected familial cancer syndrome and who have previously received uninformative genetic testing. Simple and complex genetic changes are looked for and assessed from a targeted panel of 101 genes of which are known to cause familial cancer. These changes are reported back to the patient’s treating clinicians.
The ICCon project is part of the Australian Genomics Health Alliance (Australian Genomics). Australian Genomics is a collaboration of more than 80 organisations, both nationally and internationally, which aims to integrate genomic medicine into mainstream healthcare. Australian Genomics launched in 2016 with the award of a $25 million grant from the NHMRC entitled Target Call for Research into Preparing Australia for the Genomics Revolution in Healthcare.
The Medical Genomics team is characterising genetic determinants underlying response and resistance to cancer immunotherapy. Through whole genome and RNA sequencing, we are able to identify tumor specific neoantigens that can elicit T-cell responses in cancers. Through Immunogenomics, we are able to understand the genomics of tumor cells and the properties of immune cells in the tumour microenvironment. Through further research we can uncover how tumours may prevent immune attack and why. We seek to better understand the tumour microenvironment and how it may contribute towards tumour growth. Lastly, we can uncover new techniques in patient screening to see who would benefit most from immunotherapies during the treatment of their disease.