Discovery of rare cancer risk variants

Discovery of rare prostate cancer risk variants using linkage, whole genome sequencing and imputation

Degree type


Closing date

25 September 2023



Citizenship requirement

Domestic / International

About the research project

Prostate cancer is the most commonly diagnosed non-cutaneous cancer in Tasmanian men and is associated with significant morbidity and poor quality-of-life in a large proportion of patients.  Genetics has great potential to transform and improve the way individuals are screened, diagnosed and treated for disease, as evidenced in several common cancers such as breast and colorectal cancer.  Implementing gene-based advances has been slower for prostate cancer, despite evidence that there is a strong genetic component to prostate cancer development.

The aim of this bioinformatics project is to discover rare prostate cancer risk variants that have a role in disease development and may inform screening, diagnosis and/or treatment strategies for Tasmanian men.  This project will use a range of genetic data, including genome-wide array data and whole genome sequencing (WGS) data, and various analysis methods/tools.  Essentially, the candidate will select Tasmanian prostate cancer pedigrees with WGS data and perform linkage analysis to identify regions of the genome that may contain risk variants.  WGS data from these regions will then be examined using various bioinformatics tools to identify rare, putative risk variants.

In parallel to the above, the candidate will use existing Tasmanian whole genomes to prepare reference panels for imputation.  Different methods will be used to prepare the reference panels:

  1. For imputation of population-based samples, Tasmanian genomes will be added to an existing reference panel e.g., TOPMed, in the Michigan Imputation Server; and,
  2. For imputation of familial samples, a custom reference panel will be created using bioinformatic tools within e.g., the Michigan Imputation Server or IMPUTE2.

Imputation will then be performed on genome-wide data from population-based and familial samples using population-based (e.g., Michigan Imputation Server) or familial (e.g., GiGi, FImpute, Ped_Pop) imputation programs, respectively, to identify additional carriers of the putative, rare risk variants identified through linkage analyses.

Primary Supervisor

Meet Dr Liesel Fitzgerald


Applicants will be considered for a Research Training Program (RTP) scholarship or Tasmania Graduate Research Scholarship (TGRS) which, if successful, provides:

  • a living allowance stipend of $31,500 per annum (2023 rate, indexed annually) for 3.5 years
  • a relocation allowance of up to $2,000
  • a tuition fees offset covering the cost of tuition fees for up to four years (domestic applicants only)

If successful, international applicants will receive a University of Tasmania Fees Offset for up to four years.

As part of the application process you may indicate if you do not wish to be considered for scholarship funding.

Other funding opportunities and fees

For further information regarding other scholarships on offer, and the various fees of undertaking a research degree, please visit our Scholarships and fees on research degrees page.


Applicants should review the Higher Degree by Research minimum entry requirements.

Ensure your eligibility for the scholarship round by referring to our Key Dates.

Additional eligibility criteria specific to this project/scholarship:

  • English language score must be above minimum entry requirements for this project
  • Applicants must be able to undertake the project on-campus

Selection Criteria

The project is competitively assessed and awarded.  Selection is based on academic merit and suitability to the project as determined by the College.

Additional essential selection criteria specific to this project:

  • Background in bioinformatics and/or statistics

Additional desirable selection criteria specific to this project:

  • Background in medical research

Application process

  1. Select your project, and check that you meet the eligibility and selection criteria, including citizenship;
  2. Contact Dr Liesel Fitzgerald to discuss your suitability and the project's requirements; and
  3. In your application:
    • Copy and paste the title of the project from this advertisement into your application. If you don’t correctly do this your application may be rejected.
    • Submit a signed supervisory support form, a CV including contact details of 2 referees and your project research proposal.
  4. Apply prior to 25 September 2023.

Full details of the application process can be found under the 'How to apply' section of the Research Degrees website.

Following the closing date applications will be assessed within the College. Applicants should expect to receive notification of the outcome by email by the advertised outcome date.

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