NEW CASE STUDY: Life-changing work investigating rare diseases is carried out by talented researchers who rely on some of the world’s most powerful technology and network connectivity.
From the age of three, a boy called Alan’s life was severely restricted by an immune disorder that made bleeding almost impossible to stop and began to destroy his blood cells, threatening his life.
Alan and his family had their genomes sequenced as part of a study to better understand and diagnose rare immune conditions at the Garvan Institute of Medical Research. The study was run in collaboration with hospitals and Garvan’s Kinghorn Centre for Clinical Genomics (KCCG), the largest genome sequencing centre in the Southern Hemisphere.
KCCG’s genome sequencers are some of the most powerful on the planet, capable of sequencing more than 15,000 whole human genomes a year. Every day, KCCG generates at least four terabytes of data — equivalent to around 1,600 hours of high-definition video streaming.
Working through the sequencing data for Alan and his family, the team’s clinical geneticist struck gold: a gene called LRBA. Alan’s genome contained two exceedingly rare disease-causing variants of the LRBA gene, one from each of his parents.
With the diagnosis, doctors could understand what was causing Alan’s condition: missing molecules that act as a brake on the immune system, causing it to ‘go rogue’ and attack normal body tissues.
As luck would have it, researchers in the US had recently separately identified a drug that mimics the function of the immune system ‘brake’, and Alan recovered rapidly in the weeks after starting the drug.
Alan’s life-changing diagnosis was made possible by a behind-the-scenes high-performance computing environment that has been tailored for genome informatics.
The data produced by whole genome sequencing is highly complex and goes through multiple stages of analysis and quality control. Some of this is done at Garvan, while other stages are run at scale at dedicated supercomputing facilities including the NCI supercomputer in Canberra.
Once processed, the data is accessed by national and international researchers who analyse it in a secure environment — either the NCI supercomputer or another high-performance cloud computing infrastructure.
AARNet partnered with UNSW IT and Garvan to design and deploy the network infrastructure required for the sequencing centre.
Dr Warren Kaplan, Garvan Chief of Informatics, explained that a recently implemented high-speed AARNet link connects Garvan to the NCI supercomputer for faster access to data than ever before.
“There are more than 80 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 also require a scalable network to meet our needs into the future.”
Jul 15, 2019