AARNet and UNSW IT collaborated to develop a specialised high-performance network for the Garvan Institute of Medical Research’s human genome sequencing facility.
AARNet collaborated with the IT departments of the University of New South Wales Australia (UNSW) and the Garvan Institute of Medical Research to develop a specialized high-performance network for Garvan’s Kinghorn Centre for Clinical Genomics (KCCG). This facility, the largest genome sequencing centre in the southern hemisphere, provides Australian genomics researchers with cost-effective whole human genome sequencing.
Genomics is generating new insights into the genetic causes of diseases such as cancer, diabetes, heart disease, and congenital disorders, and promises to transform healthcare.
In 2003 the international Human Genome Project announced the first sequence map of a human genome, spending 13 years and US$3 billion to do it.
Today, Garvan’s KCCG is able to sequence 150 whole human genomes every 3 days, at a cost to Australian researchers of less than A$2,000 per genome.
At full capacity, the centre can sequence 18,000 whole human genomes per year and is expected to generate in excess of 4.5 petabytes of data over the next three years.
Dr Warren Kaplan, Garvan’s Chief of Informatics says at full capacity KCCG will be moving at least 4 terabytes of data per day from the sequencing centre to the National Computational Infrastructure (NCI) in Canberra.
UNSW IT partnered with AARNet for the design and deployment of the network infrastructure required for the sequencing centre. The network provides high-speed interconnections between Garvan/UNSW and the NCI supercomputing facility.
“There are more than 70 Garvan bioinformaticians working with local and international collaborators on genomic data, and we have mind-bogglingly large amounts of genomic information that needs to be moved over the AARNet network for analysis and storage at the NCI. The volume of data is increasing exponentially so we require a scalable network to meet our needs into the future,” says Dr Kaplan.
Researchers from across Australia and around the world will be able to analyse their Garvan-generated genomic information in a secure environment by using the NCI’s supercomputer or high-performance cloud computing infrastructure.
“The reality is, we at Garvan are moving towards being very connected to the world and we see AARNet as the provider of the underlying fabric that makes it all happen,” says Dr Kaplan.
In addition, Garvan is creating a reference collection of healthy human genomes from participants in existing longitudinal study cohorts. The Medical Genome Reference Bank (MGRB) project is part of a $24 million genomics research collaborative funded by the NSW State Government.
The size of the datasets means that downloading them to the researcher’s laboratory is impractical. Instead, researchers will access and analyse the data through tools and computing facilities underpinned by AARNet at NCI.
With some of the most cost-effective genome sequencing facilities in the world, and genomic collections of international importance such as the MGRB, Australian researchers are positioned to take a leading role in emerging genomics research.
“We might be doing the genome sequencing. But we’re doing it on behalf of the genomics researchers of Australia. And we have a responsibility to them: to be able to say with regards to the challenges—be it storage, be it computing—we have addressed those. You do not need to worry about that. And that’s really the big advantage to us.”
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“The reality is, we at Garvan are moving towards being very connected to the world and we see AARNet as the provider of the underlying fabric that makes it all happen.”