NEW YORK – Researchers from the University of British Columbia and BC Children’s Hospital Research Institute are working to improve access to genomic medicine for Indigenous peoples in Canada.
Presenting at the Advances in Genome Biology and Technology (AGBT) annual meeting last week, Solenne Correard, a research associate at UBC, offered details on the effort, called Silent Genomes Project.
According to Canada's 2021 census, Indigenous communities, which comprise First Nations (FN), Inuit, and Métis, make up roughly 5 percent of the country's population.
"There is great diversity within and between the Indigenous groups," said Correard, who kicked off her presentation with an acknowledgment that this year’s AGBT took place on Indigenous land. "But all of them share challenges … they have unequal access to healthcare, including genetic care."
Despite recent advancements in genomic sciences and medicine for other Canadians, Correard pointed out, Indigenous peoples in Canada still largely have limited access to high-quality genomics healthcare. This is due to a plethora of adversities, such as geographic barriers, eligibility criteria, racism, a history of research transgressions, and a lack of representation in databases, she added.
Launched in 2018, the Silent Genomes Project has four areas of activities to bridge this disparity gap, Correard said, adding Illumina made in-kind contributions of undisclosed value to the project.
The first activity is to engage with First Nations, Inuit, and Métis members to establish guidelines for the safe governance of biological samples and genome data.
Another area is to address barriers to accessing genetic and genomic healthcare as well as to bring genomic testing to at least 200 Indigenous children with suspected genetic disorders. In addition, the project aims to develop an Indigenous Background Variant Library (IBVL) that will contain genetic variations from a diverse group of participants.
Lastly, the project plans to assess the effectiveness of the IBVL and to utilize the database to augment the diagnosis and genetic care quality for Canadian Indigenous children and adults.
During her presentation, Correard highlighted some of the efforts the team has made so far.
For example, the project established a national clinical network that contains 10 recruitment sites across Canada. In addition, the team adopted video call appointments and accepted verbal consent so that participants do not have to travel to a center to participate in the study.
As of November of last year, 81 Indigenous families with someone suspected to have a genetic disorder were enrolled for whole-genome sequencing, Correard said, and 64 of them have undergone level one analysis of their genomes, which looks at SNVs, structural variants, coding regions, and genes known to be implicated in rare diseases. Another 17 families have received level two analysis, which assesses more complex genetic variants and noncoding regions.
Level one analysis led to a probable or definite diagnosis in 25 percent of cases. However, for two-thirds of the variants that were included in the reports, the interpretation would have been better if accurate population allele frequencies were available, Correard said.
"That shows the importance of activity three, which is about building an Indigenous Background Variant Library," she said.
The plan for IBVL is to include DNA samples from about 900 individuals from the Canadian Alliance for Healthy Hearts and Minds biobank, she said. In addition, the database plans to include DNA samples from 200 Indigenous individuals from the east and west coasts of Canada, where diverse Indigenous populations reside.
To establish its governance framework, the project also created the Silent Genomes Indigenous Rare Disease Diagnosis (S-GIRDD) Steering Committee.
Bringing in various community stakeholders to the table — including Indigenous elders, community members with connections to genetic conditions, Métis National Council, First Nations Health Authority, and First Nation members — the objective for the steering committee, is to provide cultural oversight and strategic advice to the creation, implementation, and utilization of IBVL.
As the project unfolds, DNA samples from Indigenous participants will be sequenced at the Genome Sciences Center in Vancouver, Correard said.
To ensure ownership of the data stays within the Indigenous communities, she said the Silent Genomes Project adheres to a "DNA on loan" principle. "The data or the DNA is never going to belong to the university, the research, and the sequencing center," she explained. "All of those concepts were to ensure that Indigenous peoples’ data sovereignty is maintained."
After sequencing, variant analysis on the samples is carried out by BC Children's Hospital Research Institute, which has also developed a customized variant catalog pipeline using open access software, Correard said.
As for data sharing, for now, the steering committee agreed on an "intermediate model," where researchers who wish to gain access to the variant library have to agree that the data can only be used for diagnostic purposes and not for publication.
"This project is not just about creating the Indigenous Background Variant Library," she said. "It's really about community engagement and partnering with Indigenous communities to build the governance model to decide how will we use the Indigenous genomic data."