A selection of Indigenous genomics papers from 2023

27 March 2024

The year that was: a selection of Indigenous genomics papers from 2023

You want to catch up with the Indigenous Genomics literature, but you simply do not know where to start… We heard you! Here is a selection of research highlights of 2023 from Australia and abroad, pulled together by Associate Professor Bastien Llamas.

Publications by or involving ALIGN members

The National Centre for Indigenous Genomics led two companion papers—involving several other ALIGN members—that not only contribute to the global knowledge base of human genomics but also pave the way for more inclusive research practices that respect and incorporate the needs, values, and knowledges of Indigenous peoples. Based on long-term engagement with four Aboriginal communities, the first contribution (Silcocks et al., Nature) details a high proportion of previously undescribed genetic variation and a high diversity of genomes among Indigenous Australians. The second study (Reis et al., Nature) leverages the power of long-read DNA sequencing—the most recent technology available to sequence genomes— to look at complex genomic features and uncovers a large number of previously unannotated variants often unique to each community. Overall, NCIG’s research highlights the remarkable breadth of Indigenous Australian genetic diversity and its uniqueness—not only compared to the rest of the world but also across communities.

But can this unique genetic diversity have significant health outcomes? A separate whole-genome sequencing study investigated genetic variations that affect drug response among the Tiwi people (Samarasinghe et al., Frontiers in Pharmacology). Strikingly, many individuals carry actionable genetic variants involved in the metabolism of drugs commonly used to treat pain, cancer, and chronic cardiac, metabolic, and mental diseases. Using the same data, researchers identified genetic variants associated to kidney function that are either absent or rare in the large UK BioBank population (Arunachalam et al., Genome Medicine). Altogether, these results emphasise the need for tailored personalised medicine approaches that would contribute to improved health outcomes for the Tiwi people.

Advancing diagnosis and research for rare genetic diseases in Indigenous populations is the focus of ALIGN members involved in the International Rare Diseases Research Consortium (Baynam et al., Nature Genetics). Their paper underscores the crucial need for equitable healthcare and identifies solutions to tackle the health inequity faced by Indigenous people globally, such as integrating Indigenous perspectives into genetic and genomic research.

Some ALIGN researchers explored the potential of sedimentary ancient DNA (sedaDNA) to deepen the understanding of Australia’s ecological and human history (Lewis et al., Molecular Ecology Resources). They discuss the technical aspects of sedaDNA, its applications in non-ecological and ecological studies, and the significance of aligning research practices with Indigenous values and protocols.

If you are less interested in the technical aspects of Indigenous genomics and more interested in the ELSI implications, a systematic review of the literature focusses on the engagement of Indigenous communities in genomics research (Gwynne et al., Human Genetics). It addresses historical issues in genomics research in high income countries related to Indigenous peoples, ranging from exploitation to a lack of effective engagement. The paper highlights the importance of engaging with Indigenous individuals and communities in a collaborative manner that respects cultural values and sovereignty, to ensure they benefit from advances in medical research and technology. Similarly, another paper discusses the challenges and approaches for including Indigenous Peoples in clinical and genomic research, with a focus on respecting their rights, enhancing their engagement, and balancing the risks and benefits of research involvement (Waanders et al., Neoplasia). It also proposes building a community of Indigenous researchers through educational initiatives and mentorship to ensure culturally appropriate research practices.

What is happening outside of ALIGN and even Australia?

A potentially useful structured framework for conducting respectful omics research in partnership with Indigenous Australians was published last year, with the goal of protecting Indigenous interests and promoting community autonomy (Soares et al., Medicine, Health Care and Philosophy). See the Table in that paper for a list of points to consider for efficient, respectful, and sustainable engagement.

Outside of Australia, several papers discussed the need for careful, ethically responsible inclusion of marginalised communities in genomic databases. Indeed, simply adding diverse genetic data will likely not automatically translate to benefits for these populations. Some US-based authors call for a multidisciplinary approach, reshaping healthcare systems for equity, and establishing benefit-sharing models to compensate communities for their data contributions (Jabloner & Walker, The Hastings Centre Report). Other Canada-based authors promote self-governance and propose Indigenous-led, culturally appropriate health research to address disparities faced by Indigenous Peoples (Caron et al., International Journal of Environmental Research and Public Health).

But is it even ethical to generate diverse genomic data? An interesting paper suggests that generating diverse datasets is not inherently ethical and addresses the complex ethical issues that arise when attempting to diversify genomic databases to include individuals from historically underserved or minority groups (Hardcastle et al., Cambridge Prisms: Precision Medicine).

Beyond literature reviews and opinion pieces, one article involved interviews with various stakeholders in the US, aiming to understand ethical issues and develop policies that respect cultural appropriateness in research. The study delves into how Indigenous Peoples are increasing their governance and oversight over genomics research, and discusses the nuances of research regulation (Garrison & Carroll, Frontiers in Research Metrics and Analytics).

Let’s finish with a discussion of the ethical imperative and methodologies for returning genetic research findings to Indigenous communities, focusing on a case study with the Mapuche people in Chile (Arango-Isaza et al., Frontiers in Genetics). The authors advocate for collaborative approaches that respect cultural values and address historical inequalities in genomics research, emphasising transparency and community participation to ensure research is culturally sensitive and beneficial to Indigenous peoples. The paper was published shortly after the original genomic study (Arango-Isaza et al., Current Biology) as an independent piece.

Bastien Llamas is passionate about genomics and works towards making it more inclusive through his research and training and education. He is currently Associate Professor at the University of Adelaide.