Medical Genomics

Dr Nic Waddell

Group Leader &
Cancer Program Coordinator

The Medical Genomics Team analyses next generation sequence data to address clinical challenges in a variety of diseases. The approaches we take include:

  • characterising cancer genomes with short and long read sequencing
  • classification of tumours into significant subtypes
  • identification of mutational processes that underlie tumour development
  • determining genomic and transcriptomic features associated with immune response

Ultimately, we aim to take steps towards ‘personalised medicine’ to enable the diagnosis, management and treatment of patients.


Queensland Genomics




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:

  • A variety of genomics projects based on community consultation and stakeholder engagement
  • Improving accessibility of genetic health services for patients
  • Developing guidelines for researchers partnering with Aboriginal and Torres Strait Islander peoples

Cancer Genomics

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:

  1. Melanoma

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. 

  1. Lung cancer and Mesothelioma

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.

  1. Gynaecological Cancers

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.

Cancer Immunotherapy

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.


Internal Collaborators

External Collaborators

  • Andrew Barbour, PA hospital and The University of Queensland
  • Aldo Scarpa, University of Verona
  • Australian Genomics
  • Bruce Robinson, Jenette Creaney and Anna Nowak, NCARD and University of WA
  • Claire Scott, WEHI
  • David Fielding, RBWH
  • genomiQa Pty Ltd
  • Graham Mann, MIA
  • Julie McGaghgran, Genetic Health QLD
  • Max Kelsen, Brisbane
  • Pam Pollock, QUT
  • Peter Simpson, UQCCR, The University of Queensland
  • Queensland Genomics
  • Sean Grimmond, VCCC, University of Melbourne
  • Sunil Lakhani, UQCCR, The University of Queensland

We gratefully acknowledge the support of the following funding organisations, funding bodies and donors:

The Medical Genomics Group are taking steps towards ‘personalised medicine’ to enable the diagnosis, management and treatment of cancer patients

The team analyses next generation sequence data to address clinical challenges in a variety of diseases

Dr Nic Waddell heads the Medical Genomics team at QIMR Berghofer


Somatic changes to mitochondria DNA in cancer development

This project is suitable for Honours, Masters, MPhil, MD or PhD student. Background Mitochondria are membrane-bound cell organelles that are critical for energy production and cell metabolism. Mitochondria are located in the cytoplasm of cells and have their own DNA that is circular and approximately 17 kb. Aberrant mitochondrial function is a key component of […]

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