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Nigerian Population Structure, Genetic Variation Uncovered in Whole-Genome Sequencing Study

NEW YORK – A team from the US, Nigeria, and the UK has started to tease out the extensive genetic diversity that exists within and between populations in Nigeria — work that is expected to lay the foundation for future genomic research and personalized medicine efforts in Africa.

"This is another big step forward towards precision health equity, showcasing a diverse selection of individuals from numerous ethnolinguistic groups, in one of the most diverse population centers on earth," senior and co-corresponding author Abasi Ene-Obong, founder and CEO of the Washington, D.C.-based health technology company 54gene, said in an email.

Ene-Obong added that the new research represents roughly 10 percent of ethnolinguistic groups found in Nigeria and emphasized that there are "far more populations than this in Nigeria and Africa in general, each with their unique exposures, adaptations, [and] selective histories, [who] have been uniquely influenced by disease and environment."

As they reported in Cell Genomics on Tuesday, the researchers sequenced the genomes of 449 Nigerian individuals from 47 self-reported ethnolinguistic groups recruited at dozens of study sites spanning 18 states across the country. They identified around 36 million SNPs, small insertions, or small deletions that informed their analyses of population structure, genetic variation, and medically relevant risk variants.

"To the best of our knowledge, this is one of the first studies in humans in Africa where a significant portion of the human whole-genome sequencing was carried out on the continent, supporting the call by many researchers that population genomics should be [co]-led by local scientists and capacity should be built in highly diverse geographic centers for the benefit of the local ecosystem and global advancements in genomic sciences," Ene-Obong explained.

For population structure and other analyses presented in the study, the team compared the newly sequenced Nigerian genomes to one another and to sequences for more than 400 Human Genome Diversity Project participants from countries in Africa and beyond, as well as to high-coverage sequence data for 650 African individuals assessed at the New York Genome Center for the 1000 Genomes Project.

"In terms of population structure, we observed genetic similarity among [ethnolinguistic groups] that often or sometimes correlated with their geographic location," Ene-Obong said.

The analyses highlighted clusters of genetically similar ethnolinguistic groups in regions of southern Nigeria that differed from groups in central and west-central Nigeria and other central western groups and groups in northwestern Nigeria. On the other hand, individuals from Fulani, Hausa, and Kanuri groups tended to be more genetically heterogenous and carried ancestry from North Africa and Europe.

Along the way, the investigators identified a slew of previously unappreciated genetic variants or variants that appear to be rare in European populations profiled in the past. Even so, they found that rare variants appeared to be more common in some ethnolinguistic groups than others.

For example, Fulani and Kanuri individuals had somewhat lower rare variant rates than other groups in Nigeria, potentially owing to enhanced ancestry from North Africa and Europe that turned up in the team's ancestry analyses. Unknown variants were also less common in groups from more extensively studied populations from southern Nigeria.

The team noted that the new sequence data may be particularly informative when it comes to understanding potential contributors to noncommunicable diseases such as cancer, heart disease, or type 2 diabetes, and for developing related personalized medicine strategies for treating these and other conditions in Nigeria and other parts of Africa.

The authors also explored frequencies of pharmacogenetic variants across the ethnolinguistic groups profiled, noting that the Nigerian genome results "have implications for precision medicine across global populations, such as prioritization of more at-risk groups for screening or population-specific drug dose calibration."

While the genome collection contained 134 variants classified as pathogenic in ClinVar, Ene-Obong noted that genome sequencing efforts like this one are expected to provide more precise pathogenic or likely pathogenic variant classifications for diverse human populations, as allele frequency estimates and disease associations are explored in a range of global populations.

The current study is also expected to inform future efforts to tease out new or rare genetic variants, population structure patterns, and disease risk contributors in populations from Nigeria and other parts of Africa as whole-genome sequencing efforts continue to expand. Ene-Obong noted that Nigeria alone is home to an estimated 300 to 500 ethnolinguistic groups.

"Our results also emphasize the utility of publicly available WGS data from undersampled African populations as a resource to enable better cataloging of genetic variation to drive initiatives in precision medicine, improvement of human reference genomes, and the elucidation of population histories," the authors wrote.

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