Cancer Genetics

The Cancer Genetics Laboratory focuses on why some people get breast cancer, and how these cancers develop from a normal cell.  Using genome wide association studies (GWAS) we have identified over 200 breast cancer risk loci. We have successfully identified some of the target genes at several of these loci. The functional mechanism behind the associations usually involves perturbed regulation of target gene transcription by risk single nucleotide polymorphisms (SNPs) lying in regulatory elements positioned some distance from the target. The nearest gene to the GWAS ‘hit’ is not necessarily the target of the association, and for some loci there are multiple gene targets. We have developed a pipeline for predicting target genes at GWAS hits but the challenge of functionally interrogating each risk locus to identify the target gene(s) is enormous.


  • performing large scale pooled CRISPR screens of all the predicted target coding and non-coding genes at these loci to identify novel breast cancer risk genes (working with Dr Sefi Rosenbluh)
  • using assays in these screens to identify genes that impact on proliferation, anchorage independence, senescence, and tumorigenicity
  • developing methods to look at the role of these genes in T-cell mediated killing and the implications for immunosurveillance
  • by identifying the normal breast cells in which the risk-associated SNPs act, we are characterizing the chromatin landscape in normal human breast cells
  • exploring opportunities for drug repositioning from knowledge of the GWAS target genes for prevention and treatment of breast cancer

Our Staff

  • Dr Jonathan Beesley, Senior Research Officer
  • Dr Sharon Johnatty, Research Officer
  • Dr Karen McCue, Research Officer
  • Dr Wei Shi, Research Officer
  • Dr Christos Xiao, Research Officer
  • Helene Holland, Data Manager
  • Debra Black, Research Assistant
  • Andrew Civitarese, Research Assistant
  • Anna Marsh, Research Assistant
  • Malcolm Lim, PhD Student
  • Oishee Chatterjee, PhD Student

Internal Collaborators

External Collaborators

  • Dr Sefi Rosenbluh, Monash University
  • Dr Kara Britt, Peter MacCallum Cancer Centre
  • Professor Melissa Southey, Monash University
  • Dr Paul James, Peter MacCallum Cancer Centre
  • Dr Roger Milne, Cancer Council Victoria
  • Professor Geoff Lindeman, Walter and Eliza Hall Institute
  • Professor Sunil Lakhani, University of Queensland
  • Professor Doug Easton, Cambridge University
  • Professor Antonis Antoniou, Cambridge University
  • Dr Kate Nathanson, University of Pennsylvania

The lab has been continually supported by NHMRC since 1992

  • NHMRC Fellowship, Program, Project, EU, Ideas and Investigator grants
  • US Army Department of Defense
  • Gray Foundation (USA)
  • National Breast Cancer Foundation


Identifying the casual genes at cancer risk loci

Suitable for PhD or Honours students. Our laboratory is involved in genome wide association studies to identify common variation underlying risk of breast and ovarian cancers. The current challenge is in the functional interpretation of genetic association data. With this aim, we use a variety of computational approaches to define potential molecular mechanisms at GWAS […]

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