Clinical Genomics and Bioinformatics Group

Research Overview

The Clinical Genomics and Bioinformatics (CGen) group is located on Level 6 of the Alfred Centre, Melbourne.

Genomic medicine is an emerging medical discipline relying on the principle that an individual’s unique genetic constitution can inform the practice of medicine, by determining disease risk and predisposition, diagnosis and prognosis, and the choice of intervention or therapeutic options.

The CGen group is leading research programs that are generating the knowledge and evidence base to enable the implementation of genomic medicine into mainstream clinical care, with a focus on cancer genomics, public health genomics, translational bioinformatics and pharmacogenomics.

Our research is currently supported by grants from the Victorian Cancer Agency (2022-2026), MRFF (Genomics Health Futures Mission, 2021-2025), NHMRC (Synergy grant, 2022-2026) and Cancer Council Victoria (Grant in Aid, 2023-2025).

The CGen group seeks opportunities for interdisciplinary collaborations with the potential to demonstrate the value and effective use of genomics in medicine.

We welcome enquiries from prospective staff (post-docs & bioinformaticians) and students (Honours & PhD), with a background in- or a strong interest in learning- bioinformatics and/or genomics.

Meet the team

Group Leader

Senior Research Staff
- Dr Jason Steen, Senior Bioinformatician
- Dr Dan Belluoccio, Genomic Analyst
- Dr Heidi Fettke, Research Fellow
Adjunct Research Staff
- Professor Sebastian Sardina (School of Computing Technologies, RMIT)
PhD students
- Mr Zhu Jun (Joshua) Law
- Mr Liêm Le
- Mr Michael Luu (co-supervision with Precision Medicine, School of Clinical Sciences at Monash Health)
- Mr Christopher Peh (co-supervision with Treg Therapies, School of Clinical Sciences at Monash Health)
Masters student
- Ms Bhavishya Santosh (Master of Data Science)
Past students
- Ms Ruby Mattingley (Bachelor of Applied Data Science)
- Ms Julide Geygel (Master of Genome Analytics)
- Mr Daniel D’Silva (Master of Genome Analytics)

Projects

Rapid technological advances, declining costs, accumulation of genomic knowledge and refinement of analytical frameworks are creating increasing demands and opportunities for genome-informed personalised medicine. We partner with academic researchers, clinicians and national research programs in the Alfred Medical Research and Education Precinct (AMREP), the Monash Health Translation Precinct (MHTP), the Melbourne Biomedical Precinct in Parkville, and beyond.

Some of the projects and collaborations can be found below.

A/Prof Nguyen-Dumont is the genomic and bioinformatics lead of several multidisciplinary teams that are leveraging next-generation sequencing technologies to enhance our understanding of the biological mechanisms underlying cancer predisposition, initiation and progression.
- Non-smoking oral cavity cancer (Collaborator: A/Prof Bingjian Feng, Utah University): this project applies exome sequencing paired with high resolution nDIA proteomic analyses of tumour and adjacent normal tissues to characterise genetic susceptibility to oral cavity cancer and identify biomarkers for prognostic prediction of young onset oral cavity cancer, in non-smoking patients.
- Adult glioma (Collaborator: Prof Enes Makalic, Monash University): this project applies a multi-omics and machine learning approach to identify genetic risk factors for adult glioma, a malignant brain cancer with one of the poorest 5-year survival rates.
The emergence of Lu-PSMA is the most significant therapeutic development in advanced prostate cancer of the past decade. In this collaboration with Prof Arun Azad, Peter MacCallum Cancer Centre, we are performing serial plasma collection in patients with metastatic castration-resistant prostate cancer treated with Lu-PSMA. We developed a custom analytical pipeline to define ctDNA biomarkers associated with prognosis, response or resistance to treatment. The ground-breaking data that we are generating will ultimately optimise and improve the efficacy of Lu-PMSA, resulting in better outcomes for men with advanced prostate cancer.
The CGen group is part of an integrated tumour neoantigen discovery platform, alongside 3 other emerging leaders in their respective disciplines at Monash University: Dr Pouya Faridi, Head of Translational Antigen Discovery; A/Prof Josh Ooi, Head of Cell Therapies, and Dr Gwo-Yaw Ho, Head of Cancer Immunology and senior medical oncologist at Monash Health.
- iMOP: the primary aim of the platform is to integrate genomics, immunopeptidomics and immunologic technologies to develop effective, novel, precision cell-based immunotherapy for patients with immunologically “cold” cancers. These patients are the hardest to treat and have otherwise limited treatment options. We have demonstrated proof-of-concept evidence for precision TCR-T in an ovarian cancer with low tumour mutational burden and are expanding our work to a cohort of pancreatic cancer specimens.
- Monash Live Biobanking (MoLBi) platform is a Monash Health-funded comprehensive repository for live brain tumour samples, integrating cutting-edge tumour profiling and pre-clinical model technologies. We will profile the immunopeptidomics landscape of brain tumours and develop precision immunotherapies to address the limited therapeutic options for brain tumours, both primary and secondary.
Piloting population genomic screening for common hereditary conditions in young adults
DNA Screen (led by Prof Lacaze, Monash University) is a national pilot study of population genomic screening for Hereditary Breast and Ovarian Cancer, Lynch Syndrome and Familial Hypercholesterolemia. The DNA Screen study recruited >10,000 participants, aged 18-40 years, between August 2022 and December 2023 who underwent genetic testing in the Precision Medicine laboratory (Prof Southey, Monash University).
The CGen group developed and optimised high-throughput laboratory and bioinformatics processes for i) targeted sequencing using a multi-gene panel, ii) the identification of high-confidence genetic variants, iii) the prioritisation and curation of medically actionable variants and iv) the result reporting to the study participants.
The CGen group develops analytical frameworks and pipelines to analyse genomic data derived from large-scale research cohorts, with the aim of characterising genomic variants and their association with disease predisposition, initiation and progression.
- BRA-STRAP (led by Prof Melissa Southey, Monash University): this is an Australia-wide study of breast cancer predisposition that brings together gene-panel data from 30,000 adult Australian women of all ages, across the breast cancer risk spectrum, with and without a diagnosis of breast cancer.BRA-STRAP has generated Australian-specific, population-based estimates of risk for genes that are commonly included on panel tests for breast cancer predisposition.
- ASPREE genomics (led by Prof Paul Lacaze, Monash University): the ASPREE Healthy Ageing Study collected biospecimens from more than 15,000 healthy, elderly participants. The CGen group collaborates with ASPREE to interpret the genomic variation observed in these participants and their risk of developing various conditions.

Department of Cancer Medicine

Medicine, Nursing and Health Sciences

Clinical Genomics and Bioinformatics Group

Research Overview

Meet the team

Group Leader

Projects