Discovering effective treatments for cancer is like finding a needle in a haystack, requiring analysis of hundreds of thousands of DNA sequences; a mission researchers at the University of Adelaide have made their life’s work.
Professor David Adelson, head of Bioinformatics, and Professor Hamish Scott, head of the Centre for Cancer Biology (CCB), and their team are analysing DNA sequences with the aim of identifying which chemical is likely to be most effective against a particular cancer.
“If we can identify the mutation that causes a particular cancer we can select a drug that is most likely to be effective against it,” Professor Scott said.
The answer lies in the DNA of the tumours.
“Breast cancers, for example, used to be grouped together because they manifested themselves in the breast but that is irrelevant to the treatment, which is now increasingly based on the genetics of the tumour.”
DNA sequencing generates huge masses of data requiring immense computing power and capacity. The team working under Professors Scott and Adelson generate 600 gigabases of DNA sequences, equivalent to about 100 human genomes, in just two weeks.
In South Australia this work would not be possible without access to eResearch SA’s high-performance computing and data storage infrastructure.
Professor Adelson and his team are partners with and clients of eResearch SA.
“Getting useful information from such high volumes of complicated data requires huge computing power and many researchers simply don’t have access to the computing infrastructure needed to analyse their data,” Professor Adelson said.
“eResearch SA has the power and capability needed to extract meaningful information from sequencing results and other data sets.
“For our work in cancer genomics, the ability to store and retrieve high volumes of data securely and search, compare and analyse them quickly is vital.
“Storage in a dedicated, managed facility like eResearch SA’s data storage facility minimises the risk of data loss or corruption.”
For the cancer genomics project eResearch SA hosts and maintains a dedicated CCB computer the team can access at any time.
“This arrangement enables us to do a lot of work in house, including manipulation of cancer genomes, generation of data and data analysis,” Professor Scott said.
“Until the eResearch SA facilities became available much of this work was outsourced.
“Being able to do it in house means we can train researchers in areas like experiment design and data analysis, which allows us to build the capacity of our team.
“Top-quality research institutions need these capabilities in their personnel.”
Professors Scott and Adelson are excited about what eResearch SA’s new supercomputer, Tizard, will bring to their research.
Professor Adelson was one of the Chief Investigators involved in writing the grant application for Tizard, which is six times faster than eResearch SA’s previous supercomputers and the fastest machine South Australia has ever had.
“Tizard will increase the processing capacity and computing power available through eResearch SA’s high-performance computing service which will make our research even easier and allow us to get results faster,” Professor Adelson said.
“For example, previously it took three months to sequence the DNA of a mouse. With Tizard we can sequence 20 mice in that time.”