The Department of Medical Genomics provides a DNA genetic testing service as well as a clinical genetics service. It work encompasses a broad range of genetic disorders and it provides a DNA testing service for NSW. A number of referrals for DNA testing come from interstate or from New Zealand.
A number of the DNA testing programs are ongoing collaborations with other Departments/Centres within RPA Hospital including the cancer testing and research program (collaboration with Department of Tissue Pathology RPAH) and porphyria or familial hypercholesterolaemia DNA testing and clinical service programs (collaboration with the Department of Clinical Chemistry RPAH).
An interesting collaboration in porphyria involved researchers in Memphis, USA which allowed some changes in the porphyria genes being tested in vitro and in vivo using various models. This work was reported in 2016 (see Fakuda et al 2016). A long standing research project in prosopagnosia has involved gene isolation and detection in what is expected to be a complex genetic disorder. Ongoing work funded by the NHMRC has allowed the development of a pharmacogenetics/pharmacogenomics strategy to test for drug response to medical/drug treatment of alcohol dependence and identify genetic factors that might impact on outcomes.
Cancer research (Researchers involved in this study: B Yu, C Kavanagh, Charles Prabhakar and W Cooper. Departments of Medical Genomics and Tissue Pathology RPAH).
Research Project: Development of rapid onsite processing of fresh biopsy and blood/plasma samples for comprehensive mutation testing and future studies.
- EBUS (Endobronchial Ultrasound) biopsy samples (fresh tissue) were collected in 47 patients with potential lung cancer, among which were 3 duplicate samples, 6 not originated from lung, 2 not malignant, 4 yield insufficient DNA, and 2 failed QC.
- Meanwhile 5 mL peripheral blood samples were received in 40 cases.
- The analysis of 26 pairs of the biopsy and normal blood DNA from the above cases were completed using both MassARRAY OncoFOCUS and Qiagen Human Lung Cancer Panel (a target gene panel covering 333 kb genomic regions).
- Circulating cell-free DNA extraction was established. Plasma cell-free DNA was extracted from the above blood samples. Somatic mutation testing was carried out using MassARRAY UltraSEEK method and NGS Swift 56G Panel. However, this part was not completed due to lack of funding for NGS analysis.
Prosopagnosia (Researchers M Hinchcliffe, Huong Le, R Trent, Dept of Medical Genomics in collaboration with the Macquarie Centre for Cognitive Science (MACCS) and University College of London, Department of Psychology).
We have been examining individuals with congenital prosopagnosia, otherwise known as 'face-blindness' - a condition where individuals have significant difficulty recognising people by their faces alone. Sufferers frequently rely on other means to identify people such as voice, gait, clothing and hairstyle and usually have difficulty meeting acquaintances out of usual context. The research has been using next generation DNA sequencing, in depth bioinformatic analysis and genetic segregation studies. The aim of the study is to discover a gene that may be causally linked to the condition. Congenital prosopagnosia is surprisingly under-recognised in the medical community as it affects approximately 2% of the population with no racial bias. About half of the participants involved have other family members in the study for genetic linkage analysis. Prosopagnosia appears to have an autosomal dominant inheritance pattern.
Pharmacogenetics and pharmacogenomics (Researchers N Luquin, R Trent, Dept of Medical Genomics RPAH and collaborators in Department of Drug and Alcohol, RPAH)
The medical, psychological and social sequelae of alcohol dependence are recognised as major public health concerns. Australia-wide, alcohol misuse accounts for an annual economic burden estimated at $30 billion and it is now the major cause of drug-related death. Current approaches to treatment have limited efficacy. A front line of treatment development has been pharmacotherapies. This study examines a novel pharmacotherapy, topiramate, in the Australian context. A double-blind randomised controlled trial to examine the clinical and cost effectiveness of topiramate versus an active control (naltrexone), stratified according to predictive polymorphisms, in an attempt to improve treatment outcomes for alcohol dependence. This is the first prospective pharmacogenetic trial of topiramate world-wide and the first adequately powered trial of topiramate versus an active control (naltrexone). This trial has the potential to provide more effective treatment for alcohol use disorders, to define those most likely to respond and to lessen the impact of the common comorbidities. The project will test the potential transformation to personalised medicine and thus change the way we treat alcohol problems.
- Dr M Hinchcliffe, prosopagnosia
- Dr Huong Le, prosopagnosia
- Prof R Trent, prosopagnosia, porphyria, pharmacogenetics
- Dr N Luquin, pharmacogenetics
Publications and Presentations
- Yu B. Importance of mutation analysis in anti-cancer therapy. In: eLS (Encyclopedia of Life Sciences). John Wiley & Sons Ltd, Chichester. 2016; http://www.els.net DOI: 10.1002/9780470015902.a0026561
- Fukuda Y, Cheong PL, Lynch J, Brighton C, Frase S, Kargas V, Rampersaud E, Wang Y, Sankaran VG, Yu B, Ney PA, Weiss M, Vogel P, Bond PJ, Trent RJ, Ford RC, Schuetz JD. Plasma membrane exporter, ABCB6, modifies severity of porphyria. Nature Communications (Nat Commun) 2016; 7:12353. PMID: 27507172
- Kakavand H, Walker E, Lum T, Wilmott JS, Selinger C, Smith E, Saw RP, Yu B, Cooper WA, Long GV, O'Toole SA, Scolyer RA. BRAF^V600E and NRAS^Q61L/Q61R mutation analysis in metastatic melanoma using immunohistochemistry. Histopathology 2016; 69:680-686 PMID: 27151331
- Lyle M, Haydu LE, Menzies AM, Thompson JF, Saw RP, Spillane AJ, Kefford RF, Mann GJ, Cooper WA, Yu B, Scolyer RA, O'Toole SA, Long GV. The molecular profile of metastatic melanoma in Australia. Pathology 2016; 48: 188-193. PMID: 27020391
- Russell P, van der Griend R, Anderson L, Yu B, O'Toole SA, Simcock B. Evidence for lymphatic pathogenesis of endosalpingiosis. Pathology 2016; 48:72-76 PMID: 27020212
- Luk PP, Weston JD, Yu B, Selinger CI, Ekmejian R, Eviston TJ, Lum Trina, Gao K, Boyer M, O'Toole SA, Clark JR, Gupta R. Salivary duct carcinoma: Clinicopathologic features, morphologic spectrum, and somatic mutations. Head & Neck 2016; 38 (S1):E1838-47. PMID: 26699379
||YEARS total $$
||CIs: Prof Paul Haber, Dr Kirsten Morley, Prof Maree Teesson, Prof Henry Kranzler, Dr Marian Shanahan, Prof Ron Trent, A/Prof Andrew Baillie, Dr Natasha Luquin
||Defining the Clinical Role of Topiramate for the treatment of Alcohol Dependence in Australia
Contact details for department
Head of Department: Prof Ronald J A Trent
Department/Unit: Medical Genomics
Telephone: (02) 9515 7514
Facsimile: (02) 9515 6133