Updated at: 06/12/2013 at 10:51 am
The Victorian Life Sciences Computation Initiative (VLSCI) is often the channel for huge datasets on their way to new discoveries.
And the new x86 BARCOO machine, ideally suited to high-memory tasks in bioinformatics, is the latest offering to help big collaborative genomics projects.
In cancer research, when no single gene can explain genetic susceptibility, researchers need to sift through clues from variants in the same genes from multiple families. This means samples obtained over years of clinical record-keeping and the datasets required to find the potential sources are, necessarily, big.
This is where bioinformaticians can help. For example, the Melbourne-based COMPLEXO consortium, was recently searching large datasets from around the world to find new breast cancer susceptibility genes. The aim is then to genotype the putative cancer-causing genetic variants in 400,000 individuals, including 100,000 breast cancer cases and controls – on a custom OncoArray – to determine which are associated with breast cancer risk.
All teams were facing a deadline, the QIMR systems housing the data were struggling and at full capacity. So Dr Maria Doyle, Bioinformatician at the Peter MacCallum Cancer Centre (Peter Mac) began helping colleagues in a collaboration involving Professor Georgia Chenevix-Trench, QIMR Berghofer Medical Research Institute, Professor Melissa Southey, University of Melbourne and Professor Ian Campbell and Dr Ella Thompson from Peter Mac.
Maria called on bioinformaticians at VLSCI’s Life Sciences Computation Centre to ask to use their compute allocation and expertise, and sent the data down to be processed.
The work was done, the deadline met, and genetic variants of interest were submitted for inclusion in the new OncoArray design.
It’s expected that the results will be as impactful as those from the previous customised iCOGS genotyping chip published in a Focus issue of Nature Genetics earlier this year.
The VLSCI’s supercomputer BARCOO x86 machine, is the fourth computer in the facility. It has more than enough memory capacity to suit the kinds of bioinformatics problems faced by Maria and colleagues earlier this year. For more details: www.vlsci.org.au.