Obtaining high quality transcriptome data from formalin-fixed, paraffin-embedded diagnostic prostate tumor specimens

Lead researcher

Dr LM FitzGerald

Main finding

This study focuses on prostate cancer, the most commonly diagnosed cancer in Australian males.  Survival rates have steadily increased over the last two decades, however more than 3000 men continue to die of this disease each year.  Unfortunately, there are currently no definitive clinical characteristics or tests that can predict at diagnosis whether a patient is at risk for fatal disease.  Consequently, many men undergo invasive treatment “just in case” and can end up with debilitating, long-term treatment side effects.  The overall aim of Dr FitzGerald’s recent project was to detect gene expression changes in the tumour tissue of patients that are associated with fatal prostate cancer. In particular, they wanted to detect changes in diagnostic tumour samples to identify biomarkers that could be tested before invasive treatment had occurred.  However, this presented a huge challenge; diagnostic samples generally consist of formalin-fixed, paraffin-embedded (FFPE) needle biopsies which are of very small quality and quantity. Dr FitzGerald (from the Menzies Institute of Medical Research, University of Tasmania and the Cancer Council Victoria) worked closely with Ms Vasic and Ms Gould to optimise a transcriptome-specific protocol that could be applied to such tissues. This has resulted in a recent publication in Laboratory Investigation. More importantly, however, is the fact that this protocol can be applied to any diagnostic FFPE sample, facilitating the discovery of biomarkers for a range of cancers.



Research group

Technology Platforms and Capabilities


FitzGerald LM, Jung CH, Wong EM, Joo JE, Gould JA, Vasic V, Bassett JK, O'Callaghan N, Nottle T, Pedersen J, Giles GG, Southey MC

Journal and article title

Disease/health impact

Prostate cancer

Other points of interest

This work was supported by a Cure Cancer Australia/Prostate Cancer Foundation of Australia Young Investigators Grant.