2003 – $1.1 million research grant

Types of Cancer: Pancreatic Cancer, Leukaemia, Lung Cancer, Head

Research Institution: Garvan Institute of Medical Research, NSW

Director of Research: Professor Rob Sutherland

Feature Outcome:

Establishment of the Australian Cancer Research Foundation Unit for Molecular Genetics of Cancer. The purchase of major equipment including a laser microdissection system and computer, mutation detection technology, DNA analysis equipment and mutation detection technology. The dedicated unit will provide an additional capability in the search for cancer susceptibility genes. The ACRF Unit for Molecular Genetics of Cancer was officially launched by the Prime Minister of Australia, the Hon John Howard MP, on May 16, 2005. Click here for the full media release.

Research Focus: The development of a state-of-the-art, world class facility to genotype cancer, identifying patients with a predisposition to a variety of cancers including prostate, colorectal, breast and ovarian. Development of new gene markers of cancer risk, cancer diagnosis, disease progression and therapeutic responsiveness. Click here for the latest discoveries from the unit.

Further Details / Outcomes:

The Australian Cancer Research Foundation (ACRF) Unit for the Molecular Genetics of Cancer was established in 2003, when the Cancer Research Program at the Garvan Institute of Medical Research and the St Vincent’s Hospital Cancer Research Consortium were awarded $1.1 million for the purchase of state-of-the-art molecular genetic technology.

The ACRF unit is housed in three laboratories within the Cancer Program. Also included is a fourth already existing and complimentary immuno-histochemistry and in situ hybridisation facility, housing the laser capture microscope.

The purpose of the Unit is to allow high throughput assessment of germ-line and somatic mutations, single nucleotide polymorphisms (SNPs), methylation status, loss of heterozygosity (LOH) and levels of expression of a broad spectrum of genes identified through a diversity of model systems and discovery platforms already available within the program.

The establishment of the ACRF Unit is thus an instrumental component to providing the capacity within NSW to perform internationally competitive research in cancer genetics, as well as providing an additional platform to attract the best researchers and students in NSW and country-wide.

The goal of the unit is to provide technology capable of achieving high-throughput, sensitive and cost effective application to identify and document the molecular genetic mechanisms involved in the acquisition and development of cancer.

The following molecular genetic analyses are enabled by the facility:

  • genome sequencing
  • gene discovery
  • gene expression studies using quantitative real-time PCR
  • mutation and polymorphism detection
  • genotyping of repeat sequences / microstatellite instability
  • large scale methylation studies
  • large population case-control studies assessing cancer risk
  • robotic application for large scale, highly reproductive procedures such as DNA / RNA extractions, PCR and real-time PCR automation.

Below is a brief description of the technologies within the facility:

ABI 3100 Genetic Analyser / Sequencer plus GeneMapper, Seq-A and SeqScape software

The ABI 3100 Genetic Analyser is a multi-colour fluorescence-based DNA analysis system using the proven technology of capillary electrophoresis with 16 capillaries operating in parallel. It is fully automated and provides the capability of analysing hundreds of samples per day with minimal user intervention. It provides both sequencing and fragment analysis applications.

Sequenom MassArray Compact Analyser, including NanodispenserThe sequenom processes samples using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS), which can resolve mass differences down to 3 Daltons. This system is also very flexible, with multiple applications. This is the preferred system for high-throughput single nucleotide polymorphism (SNP) analysis due to its efficiency and quality of the data produced, even when performing multiple reactions.

The system is capable of performing reactions in 12-plex resulting in over 9,000 genotypes being called in a single day using only two 384 pooled-sample spotted chips. An added advantage is also its application for mutation detection (including SNP discovery and re-sequencing projects) using the MassCLEAVE chemistry, which allows automated mutation detection, reliable detection of low frequency variation often found in cancer tissue (somatic mutations), not affected by GC content as is the case with most other technologies, high accuracy and reproducibility.

The Sequenom MassArray will also be utilised for allele specific expression studies, a unique method of gene expression studies using competitive PCR, thus providing an alternative method for determining gene expression, complimentary to real-time amplification.

ABI Prism 7900HT Real-time (384-well) plus fluid card upgrade

The ABI 7900HT is a real-time PCR machine capable of high-throughput analysis and the utilisation of a broad range of chemistries, depending on your application.

This technology is predominantly utilised for gene expression studies, a fundamental experimental procedure in cancer research in particular where large number of candidate genes have been identified as markers of cancer using transcript profiling data, as is the case within the Cancer Program and St Vincent’s Hospital Cancer Research Consortium.

The ABI technology is probably the most utilised of the high-throughput real-time/quantitative PCR technologies internationally, with the 7900HT being the most recent of the upgrades, assuring high-quality data, long-term reliability, and robust performance.

This technology has also been extensively utilised for high-throughput DNA methylation studies. In addition the acquisition of the Micro fluid card upgrade dramatically reduces reagent consumption (less than 2µl reaction volume per well), thus reducing the running costs, while providing convenient, easy-to-use quantification. By utilising the fluid cards Ready-to-Use gene expression assays can be purchased and used.

Agilent 2100 Bioanalyzer

This is a vital tool for the quality control of both DNA and/or RNA where the quality of data is dependent on the quality and exact measurement of the starting material (DNA/RNA). This technology, in as little as 200pg/µl of sample, is capable of immediately determining RNA degradation and RNA contamination, as well as RNA/DNA concentrations. This level of accuracy is not attainable when utilising a normal spectrometer.

EpiMotion 5070

The EpiMotion is a recent upgrade in robotic liquid handler technology and allows contamination free DNA handling and preparation (required for all the technologies already mentioned). The use of robotics within the facility not only increases through-put, but also reduces human handling errors associated with large sample studies.


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