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54gene Leads Consortium to Sequence 100K Nigerian Genomes, Plans to Expand Continent-Wide


NEW YORK – Nigerian health technology company 54gene aims to sequence 100,000 Nigerian genomes as part of a larger goal of sequencing 500,000 genomes across the African continent.

The company, through the Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) consortium, has currently recruited upwards of 75,000 participants from across more than 100 ethnolinguistic groups and continues seeking partnerships across the continent to expand the study's reach.

The NCD-GHS recently published its strategic vision for the project in a Nature Genetics comment and announced that it had established the capacity to sequence and biobank the needed samples at scale within Africa.

The consortium, which launched in 2020, is funded by the African Centre for Translational Genomics (ACTG), an initiative established and funded by 54gene to facilitate translational genomics research and precision medicine across Africa.

People of African descent are, as a whole, underrepresented in genomic studies, often contributing to roughly 3 percent or less of most genome-wide association studies (GWAS). This makes them less likely to benefit from advances in precision medicine and genomic understanding in general.

Initiatives like the NCD-GHS "will bring Africa into that equation, which would also mean that Africans can get access to new drugs when they are developed, which is something that currently doesn't happen," said Abasi Ene-Obong, CEO and founder of 54gene.

The consortium's strategic vision largely consists of empowering African genomics by building a diverse African genomics database with which it plans to better understand and find solutions for the burden of non-communicable diseases on the continent, while ethically engaging participating communities, building research infrastructure, and fostering research leadership throughout sub-Saharan Africa.

Yaw Bediako, founder and CEO of Ghana-based cancer research firm Yemaachi, noted that the project's vision of advancing genomic research through a public-private partnership hews largely to those of similar initiatives, such as H3Africa. Nonetheless, he voiced his support for any and all projects seeking to shed light on the diversity of African genomes and the possibility that such data may help improve the quality of healthcare across the globe.

"It is a welcome signal that African genomic research capacity is growing," Bediako said.

While the database will be made publicly available for any line of research, 54gene plans to participate in many studies that make use of the database, although the company plans to focus on drug development.

"We will work with academics and other groups to put out academic papers that move the field forward," Ene-Obong said, "and we will do drug discovery, as that is where our revenue comes from."

Ene-Obong pointed to a network of partnerships with public institutions and private companies, beginning with a deal with Illumina to help establish 54gene's genetics facility in Lagos, as enabling the consortium to achieve the capacity to sequence and biobank at the scale needed for this project.

"We announced the collaboration with Illumina sometime in 2020, just before the pandemic," said Ene-Obong, "and that really gave us the opportunity to pilot [whole genome sequencing] in our labs in Africa."

Having now gained the experience of genotyping tens of thousands of samples and sequenced hundreds of thousands, Ene-Obong said that 54gene and its collaborators are now expanding regionally before extending continent-wide.

The company recently partnered with two Senegalese institutions — the National Academy of Sciences and Technology of Senegal and the Cheikh Anta Diop University — to carry out sequencing from among Senegal's principal ethnolinguistic groups. This study, dubbed Sen-Genome, aims to develop a baseline genetic characterization of the Senegalese population in support of establishing a Senegalese reference genome.

54gene has also partnered with the Tanzanian Society for Human Genomics and plans to announce other collaborators in forthcoming press releases.

"We want to [sequence] 100,000 to 200,000 whole-genome sequences in three years in Africa, not sending the samples to the US or to Europe," Ene-Obong said.

Ultimately, Ene-Obong intends to sequence at least 500,000 genomes from across Africa.

Currently, all sequencing is done using Illumina's NovaSeq 6000, while GWAS are performed with a custom array built of both commercially and publicly available sequences and sequences built by 54gene.

"It was important to develop an array that was robust enough for imputation, but also specific for our populations," Ene-Obong said. “We take information that is on some of the other arrays that are available, and we add content to it based on the whole genome sequences that we've done."

For instance, 54gene included 115,000 markers from the multi-ancestry global GWAS content found on Illumina's GDA array, ClinVar pathogenic variants enriched for African ancestry, and expression quantitative trait loci from African populations from the African Functional Genomics Resource, among other sources, alongside markers representing the most highly differentiated variants found in the company's initial sequencing of 1,000 individuals.

Additionally, Ene-Obong said that 54gene has performed WGS on about 50 ethnolinguistic groups in Nigeria which has also gone into that array design.

"As we add more ethnolinguistic groups across Africa into our reference, we will keep modifying [the array]," he said.

For now, the custom array is only being used internally, although 54gene expects to make it commercially available in the future. Although an exact cost of the array is not yet public, Ene-Obong said that it is "very competitive in terms of pricing," and that more information on that would become available in the near future.

Two key considerations in advancing the project are ensuring that participants benefit from the genetic information they provide and ensuring that they understand what the results of their sequencing may mean. To that end, 54gene sends clinical diagnostic reports to each participant’s physician and earlier this year began assembling a team to provide genetic counseling services to participants free of charge.

"As we begin to return the results, all the participants will have access to genetic counseling," Ene-Obong said.

The diagnostic reports contain actionable clinical information, with 54gene often funding the diagnostic assays used to develop them, as many areas in which participants live lack robust diagnostic infrastructure. The company has not yet begun to return sequencing results, as it is still finalizing its guidelines for reporting them.

The issue of storing and analyzing African data outside of Africa "has historically disempowered African researchers," said Aminu Yakubu, 54gene's VP of research governance and ethics. "Stopping this practice, while working to install adequate infrastructure to allow for all data generation from the samples being done in Africa, is important."

"We've been successful in supporting some of the sequencing and genotyping," Ene-Obong added, "but the next lever is to also support the development of data scientists that can support the work with teams in different parts of the world, [including] Africa."

"This project will undoubtedly be a catalyst for generating local interest in genomics in Nigeria," said Yusuf Henriques, CEO of IndyGeneUS AI, a US-based genomics firm. "It will also have great potential for developing local talent for the local biotechnology and research workforce."

Henriques expressed some concern, however, regarding the stability of research infrastructure in Nigeria.

"Power grid instability may compromise their ability to properly store and successfully sequence the number of genomes they are targeting," he said, adding that "data and sample security are also areas of concern with regards to data sovereignty."

Ene-Obong, however, sees Nigeria's power grid instability as an opportunity to invest in alternate clean energy sources.

"We currently have over 300kVA of solar energy and are growing," he said. "Essentially, we provide our own power supply by leveraging solar, batteries, and backup generators [along with] the national grid."

The company uses Identity and Access Management policies and Amazon Web Services for its cloud computing and data security.

54gene continues to seek out more collaborations with governments and private companies to expand the reach of this project throughout Africa.

"We have a few other consortiums and partnerships that are coming live across the African continent, which will be announced subsequently," Ene-Obong said. "Our goal is to build quite a robust data set from across the African continent."

Regardless of what the project uncovers, Ene-Obong hopes that it contributes to a thriving African genomics ecosystem.

"And if we're one of the major contributors to that," he said, "then that will be success."