Skip to main content
13 Dec 2023

Unique diversity of Indigenous Australians revealed by next-generation genomics

New research provides the most comprehensive picture to date of the genomic diversity within and between First Nations communities across Australia.

Ira Deveson and Andre Ries
Ira Deveson and Andre Ries

Researchers have used next-generation ‘long-read’ sequencing to reveal the highest-resolution view of the unique genetic diversity in Indigenous Australians to date, paving the way for more personalised clinical care for Aboriginal and Torres Strait Islander peoples.

Led by Dr Ira Deveson at the Garvan Institute of Medical Research in close collaboration with the ANU National Centre for Indigenous Genomics (NCIG), researchers sequenced the genomes of 121 Indigenous individuals from four communities and found that each individual carried more than 300 new ‘structural’ genetic variants unique to Indigenous Australians, indicating a richer genetic diversity than was previously thought.

The study will help identify genes that contribute to diseases, and better treatment options, by establishing genetic reference databases – in which Indigenous ancestries have until now been critically under-represented.

“Genomic information has the power to guide more personalised clinical care, but to do this we need to know what a community’s background genetic variation is, as a point of reference. With genomic medicine becoming more and more relevant in clinical practice, we want to make sure Indigenous Australians are not left behind,” says Dr Deveson, leader of the Genomic Technologies Lab at Garvan and lead author of the study published in Nature.

Next-generation genomics reveals unique genetic diversity

The researchers used a high-resolution genomics technique called Oxford Nanopore long-read sequencing to gain new insights into the genomic diversity of 121 individuals from the Tiwi Islands, Galiwin’ku and Titjikala communities in the Northern Territory, and the Yarrabah community in Queensland.

Long-read sequencing is a cutting-edge method that can accurately survey the entire human genome – including at least 10% of the genetic code that cannot be read by conventional sequencing methods – and detect ‘structural genetic variants’ that affect large segments of DNA. These variants, which occur naturally across individuals of a population, account for most of the genetic differences between individuals and may be linked to genetic disease in some families.

“We identified more than 160,000 structural genetic variants, which is more than any previous population-level, long-read study to date and discovered at least 300 structural variants in each individual that appear to be unique to Indigenous Australians,” says Dr Deveson.

The close collaboration with NCIG enabled the research, through an extensive consultation process with the communities.

Associate Professor Azure Hermes from the National Centre for Indigenous Genomics says: “Our goal is to work with and empower Indigenous Australians to take ownership of their genetic information and show them the power of genomics and the health benefits it can deliver. It’s taken us almost eight years to get to this point and has only been made possible because of guidance by Indigenous communities, careful consultation, building relationships with communities and understanding their priorities and protocols.”

The critical role of genetic diversity in healthcare

The researchers hope their study will help improve health outcomes for Indigenous Australians by providing better reference databases to identify disease-linked genetic variants.

“The four long-read genomic databases we have generated in this study are the first phase of what we hope will be a growing national program with the ANU National Centre for Indigenous Genomics,” says first author Dr Andre Reis, Research Officer in Garvan’s Genomic Technologies Lab.

During their study, the team also identified a structural genetic variant known to cause a neurodegenerative condition known as Machado-Joseph Disease in the genome of one Galiwin’ku individual. This disease is more than 100 times more prevalent among Indigenous populations in areas of the Northern Territory than the global average, but can be difficult to diagnose using existing methods.

The individual, who had consented to receiving genetic results uncovered during the study, was connected with a local genetic counsellor and clinical management services following the genetic findings. The case highlights the power of long-read sequencing for the prediction of disease risk and early mitigation.

“By identifying variants linked to higher prevalence of disease, long-read sequencing could play a critical role in boosting local healthcare efforts and represent a step towards more equitable genomic medicine,” says Dr Deveson.

This research was supported by the Medical Research Futures Fund (grants 593 MRF2016008, MRF1173594 & MRF2016124), the National Health and Medical Research Council (grants 2011277 & 2021172), and The Kinghorn Foundation.

Dr Ira Deveson is a Conjoint Lecturer at St Vincent's Clinical School, Faculty of Medicine and Health, UNSW Sydney.