World News – UA – Study reveals vast and complex diversity of African genetic variations

The study, in which six researchers from Wits were involved, shows that these newly discovered variants were found mainly among the newly sampled ethnolinguistic groups

Researchers have identified new evidence of natural selection in and around 62 previously unreported genes associated with viral immunity, DNA repair and metabolism

They observed complex patterns of ancestral mixing within and between populations, as well as evidence that the populations of Zambia were likely an intermediate site along the expansion routes of the Bantu speaking populations.

These findings enhance current understanding of migration across the continent and identify responses to human disease and gene flow as potent determinants of population variation

The study provides a major new source of African genomic data, which highlights the vast and complex diversity of African genetic variations and which will support research for decades to come

Africa is the continent with the greatest genetic diversity and this study shows the importance of African genomic data to advance science and health research It is an important step in correcting existing biases in data available for research, which hinders the study of African health problems and restricts global research »

Zané Lombard, study lead author and associate professor, Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service

Lombard led the study under the auspices of the Consortium on Human Heredity and Health in Africa (H3Africa) in association with Dr Neil Hanchard, Baylor College of Medicine, Texas, USA, and Dr Adebowale Adeyemo, National Human Genome Research Institute, Maryland, USUNE

Members of the H3Africa consortium who have contributed to this work include people from 24 institutions across Africa, including the Sydney Brenner Institute for Molecular Bioscience (SBIMB) of the University’s Faculty of Health Sciences by Wits

Dr Ananyo Choudhury of SBIMB, Dr Dhriti Sengupta, Professor Scott Hazelhurst and M Shaun Aron led the analyzes and authored the article, while Prof Michèle Ramsay, director of SBIMB, helped shape the study design and was a principal investigator who contributed samples towards this sequencing effort. on a large scale

The study revealed a wide range of genomic diversity among these genomes, with each ethnolinguistic group harboring thousands of unique genetic variants

Not only populations from the same geographic region, but even those from the same country showed a lot of variation among themselves, reflecting the deep history and rich genomic diversity across Africa

« We used a wide variety of computational techniques to better understand the population history, adaptation to the environment, and disease susceptibility of these genomes, » says Choudhury, lead author of the study and principal investigator at SBIMB

« We were able to discover more than 3 million new variants in these genomes This was after comparison with more than 1000 African genomes in public repositories, suggesting that the potential for discovering new genetic variants by sequencing African populations is still far from being saturated »

In addition to contributing to the large amount of new variation seen in African populations, the inclusion of population groups not previously studied in the study allowed scientists to add puzzle pieces to the puzzle of historical interactions established and migratory events on the continent

« The inclusion of new African genomes in our study has strongly supported Zambia as an intermediate site on the route of the Bantu migration to the south and east of the continent, » said M Shaun Aron, Principal Analyst of the Genetics Component of Study Populations and a lecturer at SBIMB

Evidence supporting the movement from East Africa to central Nigeria between 1500 and 2000 years ago has been revealed by the identification of a substantial amount of East African ancestry, particularly Nilo-Saharan from Chad, in a central Nigerian ethnolinguistic group, the Berom

« This highlights the complex historical movement of populations on the continent and the diversity of African groups, even close to proximity, » says Aron

The researchers found more than 100 areas of the genome that had likely been subjected to natural selection; a significant proportion of which was associated with genes linked to immunity

Natural selection – « selected by nature » – comes from Charles Darwin’s work for the survival of the fittest This means that when individuals are exposed to certain environmental factors (diet, viral infection, etc.) certain genetic variants can give humans who carry them in their genome an additional advantage to survive

<p frequency of genes that affect people's susceptibility to disease, ”says Dr Dhriti Sengupta of SBIMB and one of the senior analysts

In addition, the breeding signals were not homogeneous across the continent Sengupta says, “There were notable variations in the breeding signals between different parts of the continent, indicating that large scale local adaptations would have could support the migration of populations to new geographical areas, and consequently exposure to new regimes and pathogens »

Selection signals are parts of the genome that give us a signature (signal) that the specific part of the genome was under selection pressure at some point

Lombard, lead author of the article and associate professor in Wits’ division of human genetics, says: « The results are of great relevance, from research in population genetics to human history and migration, to clinical research on the impact of specific variants of health outcomes « 

Immediate next steps include further examination of initial findings and exploitation of data to represent more African populations

The researchers hope their work will lead to wider recognition of the extent of uncatalogued genomic variation across the African continent and the need to continue to include the many diverse populations in Africa in genomics research

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« The addition of genomic data from all of the world’s populations – including Africa – is essential for everyone to benefit from the health advances that precision medicine offers, » says Mr. Lombard Precision medicine – or ‘personalized’ medicine – refers to the treatment and prevention of diseases that take into account the individual variability of genes, environment and lifestyle for each person

The study represents a major step in advancing genomics research capacity in Africa Instead of analyzing African data elsewhere – as has been the general trend over the past decade – this research has been conducted mainly by local African researchers using local computer facilities

Studies like this highlight the importance of IT infrastructure and storage capacity for large data projects in Wits and South Africa

An infrastructure like the Wits Computing Cluster, established and managed by Prof. Scott Hazelhurst, Director of Wits Bioinformatics, is essential to support genomics research and the growth of African datasets. He says: “Initiatives like that the H3Africa consortium laid the groundwork to foster and encourage collaborative research in Africa, which made possible studies like these »

Professor Michèle Ramsay, Director of SBIMB, says: « This study, in a sense, heralds the availability of both infrastructure and analytical skills for large-scale genomic research on the continent »

Tags: Bioinformatics, Diet, DNA, Frequency, Gene, Genes, Genetics, Genetics, Genome, Genomics, Genomics, Laboratory, Malaria, Medicine, Metabolism, Research

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