NCI is pleased to be partnering with researchers around Australia on two Indigenous genomics projects supported by the Federal Government's Medical Research Futures Fund (MRFF). Released today, these MRFF grants will enable the further development and growth of Indigenous genomics research in Australia. NCI is building on our expertise and long-standing relationship with the National Centre for Indigenous Genomics to provide the computational and data resources that the research activities need.
All genomic data collected through these projects will be securely stored and managed at NCI according to existing, specially designed procedures. These ensure that all donor data is kept private and accessed only by authorised researchers.
NCI Director Professor Sean Smith says, “We are proud to extend NCI’s existing relationships with ANU, NCIG and the Garvan Institute of Medical Research, and provide access to the computing and data infrastructure that such big genomics projects need. We take the responsibility of hosting this data extremely seriously, and feel grateful to the Indigenous people for entrusting us with their data.”
The two successful projects are:
- Pathways to benefit for Indigenous Australians in Genomic Medicine, led by Professor Alex Brown from The Australian National University.
This project will establish a National Indigenous Genomics Network, helping to build data sovereignty and governance systems' capacity, as well as providing capacity-building workshops for the community. The project will enshrine Aboriginal and Torres Strait Islander leadership, priorities and voices in the genomic, clinical and research disciplines, and ensure that it is done with respectfully and in accordance with cultural imperatives.
- Developing a long-read nanopore sequencing platform for Indigenous genomics, led by Dr Ira Deveson from the Garvan Institute of Medical Research.
Read more about this project in the media release below, originally published by the Garvan Institute of Medical Research on Monday 26 September 2022.
New genomics resources to help Indigenous Australians find genetic diagnoses will be established thanks to support from the Medical Research Future Fund.
A team led by the Garvan Institute of Medical Research is set to establish a new genomic database for Indigenous Australians to assist with diagnosing genetic illnesses thanks to a $986,000 grant from the Federal Government’s Medical Research Futures Fund.
The project will be jointly run with the Australian National University’s National Centre for Indigenous Genomics (NCIG) and with support from Oxford Nanopore Technologies and the National Computational Infrastructure (NCI Australia).
Dr Ira Deveson, Head of Genomic Technologies and member of the Genomics Pillar and Centre for Population Genomics at the Garvan Institute, leads the project, which will use advanced Oxford Nanopore DNA sequencing technologies and Australia’s most powerful supercomputer at NCI to identify which genes might contribute to illness in Indigenous populations. [Note that NCI, together with ANU, will be providing up to 1.5 Petabytes of data storage and 10 million units of computing time to support the project.]
“Each person’s DNA is unique, our genomes contain thousands of variations that make us who we are. The hard part of using DNA to diagnose disease isn’t finding these genetic variants – it’s distinguishing which variants cause disease from the great diversity of normal, non-harmful genetic variation,” Dr Deveson says.
“Through collaboration and partnership with Indigenous communities and researchers, this project will develop new reference databases and resources to better identify harmful variants among Australia’s First Nations peoples, to ensure that they receive the correct diagnosis as soon as possible.”
A local genomic database
When someone is diagnosed with a genetic illness, their DNA is compared to a ‘reference set’ of known genetic variations that influence health and disease. These reference sets have been amassed over years with DNA samples taken from people around the world, but they predominantly include people with European heritage while Indigenous Australians are almost completely unrepresented.
Preliminary data from the National Centre for Indigenous Genomics suggests that around a quarter of all genetic variants in an Indigenous individual do not occur in people of European heritage, meaning they will be absent from reference sets.
“What that means is that at the moment when we do sequence the DNA of an Indigenous person, we have to look a lot more carefully to understand whether the variations in their genome are normal and ultimately harmless, or whether they might be contributing to disease,” says Dr Hardip Patel at the National Centre for Indigenous Genomics.
Dr Deveson agrees. “Complicating this issue further is the fact that many of the variants that may contribute to disease in both Indigenous and non-Indigenous populations occur over long or repetitive sections of DNA which are hard to detect using standard ‘short-read’ sequencing technologies,” he adds.
“Our project will use new sequencing technologies from Oxford Nanopore that can read any length of DNA fragments and which we’ve shown can reliably pick up on the variations on those long or repetitive DNA sections. This can help people with genetic diseases and their doctors find diagnoses faster and better manage the symptoms to improve quality of life.”
Collaborating with community
This study builds on the deep partnerships established by the NCIG with Indigenous communities to create new insights and health impacts beyond what is possible with existing genomics technologies.
“We’re privileged to be in a position to bring benefit to Indigenous communities through genomics and it is so important that this is done the right way,” says Professor Graham Mann, National Centre for Indigenous Genomics Director.
The team will work with eight communities from Northern and Central Australia, before expanding to other communities across the country. Thanks to the lightweight and portable nature of some of Oxford Nanopore’s sequencing technologies, like MinION, the study aims to develop the capabilities to perform genomics research with full transparency or even direct participation of Indigenous community members and local health professionals.
“Indigenous Australians harbour rich and unique genetic diversity that is currently missing from global genomics resources, limiting the usefulness of these resources for genetic diagnosis, risk stratification or carrier screening in Indigenous families. Failure to address this representation gap will lead to increasing inequity in the benefit of genomic medicine, exacerbating health disparities between Australia's Indigenous and non-Indigenous communities,” says Dr Deveson.
“Ultimately, the outcomes of this project will increase diagnostic rates for rare genetic disease and extend the benefits of the latest advances in genomic technology to Indigenous Australians,” says Dr Deveson.
Dr Ira Deveson is a Conjoint Lecturer at St Vincent's Clinical School, Faculty of Medicine, UNSW.