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High-performance computing assists medical research in SA
Working in Professor Jozef Gecz’s neurogenetics research team at the Adelaide Women’s and Children’s Hospital, Dr Mark Corbett seeks to further understand human brain function through the identification of genetic mutations that impair it.
Taking DNA from patients around the world, the team starts by sequencing a patient’s exome – 40 million characters of genetic ‘meat and potatoes’, covering individual characters up to 30 times each. The machines used to read these characters produce short reads of the patient’s DNA, with each read being the equivalent of a 60-letter word. They use eResearch SA’s supercomputers to electronically map the locations of these sequences within the 3.2 billion letter genome.
‘With the help of eResearch SA, we are able to compare each short read (60-letter word) to the human genome (3.2 billion letter word) to find out where it fits. We’re basically comparing the DNA of a patient with DNA from healthy people and seeing where the differences lie,’ Mark (far left, with a colleague) says.
‘For every patient, we generate tens of millions of reads, and comparing each read to the human genome would be impossible to do manually or on a normal desktop computer. We couldn’t do the work we’re doing without eResearch SA,’ he continues. ‘With so much data to sort, eResearch SA’s supercomputers have allowed us to take this genetic information and map out the patient’s DNA sequence onto the human genome.’
The neurogenetics team and their colleagues have contributed to the discovery of more than 50 different disease-related genes, with their research directly applicable to the 1 in 30 people who are affected with either epilepsy or intellectual disability.
Mark says, ‘Finding a genetic mutation doesn’t cure the disease, but it can be very comforting for the patient’s family to have an explanation as to why their child is unwell. If patients and their families can better understand the natural genetic mutations affecting their health, they can release themselves from any concerns about having children, or any anxious feelings about not knowing the cause.’
He continues: ‘Once we find a new gene it can also lead to other discoveries that could turn into new medications or even cures – although it’s a lengthy process. It’s great to have a facility like eResearch SA in South Australia and to be able to work with people who understand your needs. If we ask them to install a new computer program they’ll have it done within a week and will be there to assist us with any problems – eResearch SA have been very helpful and incredibly important in our research.’
eResearch SA is a collaborative joint venture between the University of Adelaide, Flinders University and the University of South Australia, and is directed by Mary Hobson. To find out more, visit www.ersa.edu.au.