A new cost-effective array designed specifically to study African populations will offer researchers unprecedented insight into the genomic and environmental causes of common diseases affecting people across the continent.
Created by genome sequencing company Illumina, in collaboration with health bodies and researchers from around the world brought together by the Human Heredity and Health in Africa (H3Africa) Initiative, it is the most comprehensive and powerful array available to date for the study of African genomics. And it’s been a long time coming.
“It is well recognized that currently available genome-wide association study (GWAS) arrays are not ideally suited to studying African populations – content either does not capture all common haplotypes efficiently, or contains variants that are uninformative in Africans,” explains Dr. Zané Lombard, co-chair of the Genome Analysis Working Group at H3Africa, a partnership between the National Institutes of Health (NIH), the African Society of Human Genetics and the Wellcome Trust, which aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of disease in Africa.
Indeed, until recently, an overwhelming proportion of studies examining genetic risk factors for disease have been carried out in European populations. It is only in the last decade that researchers have started to make any meaningful progress into understanding the genomics of Africa, which is the most genetically diverse region in the world.
This project is the next step. “The goal of this technology is to lead to a greater understanding of genomics in disease to inform strategies to address health inequity, and ultimately lead to health benefits in both Africa and beyond,” says Julie Collens, PhD, senior manager of market development at Illumina.
We caught up with Collens and Lombard to find out how.
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Elly Earls: Can you please explain in layman’s terms what an array is?
Julie Collens: The human genome has 3 billion base pairs, however most of those are consistent across all individuals within the human species. An array is a tool that researchers use to assess specific points, or loci, in the genome that are known to have variation between individuals and populations. Typically, arrays sample hundreds of thousands or a few million loci out of the 3 billion.
EE: What is special about this particular array?
JC: In order to design the content for arrays, researchers must know which particular loci are variable or important for disease risk. This array is special because it contains loci that have been identified as variable in and among African populations based on previous genetic studies in those populations.
EE: How have you managed to make it so cost-effective?
JC: Illumina has worked with the consortium to leverage relevant existing content from our multi-ethnic genotyping array (MEGA). Building on that backbone, we’ve added unique, novel content derived from research efforts of the H3Africa consortium.
EE: How important was collaboration between various different companies, associations and governments to achieving the final product?
JC: Illumina has a history of collaborating with customers and consortia to develop and design products. H3Africa consortium is the only consortium to undertake an effort of this size and scope in Africa, and played a critical role in identifying the content and driving the project forward.
Zané Lombard: Collaboration was an essential strategy. H3Africa is a continent-wide collaborative effort, including strong partnerships with the NIH, Wellcome Trust and the African Society of Human Genetics. The H3Africa custom chip task group also reached beyond this consortium to include other individuals interested in the design of an African array and who could contribute towards the content and design of the final product.
EE: Why is this needed in the African continent?
JC: Human history originated in Africa, and Africa represents the greatest amount of human diversity on the planet. Yet an overwhelming proportion of studies have been done in European populations. Since genomic database efforts have not included widespread sampling of African populations, existing research has limited the applicability of genomics to answer specific questions about disease risk in African populations. Today, there are different environmental risks in Africa (Ebola, HIV, malaria, or other disease risk) compared to other geographies. Having a better understanding of the genomic backgrounds of specific populations in specific environments is an important component in understanding disease susceptibility.
EE: How will this technology help foster genomic and epidemiological research in Africa?
ZL: This effort specifically endeavoured to produce a more appropriate product for use by H3Africa consortium members, as well as other users studying African populations. Having a more powerful array at our disposal implies that more effective studies of the genomic and environmental causes of common diseases afflicting African populations can be designed and implemented.
JC: The array will not only help researchers further understand the interaction between genomics and disease risk by specifically addressing variation in Africa, but the efforts of the consortium and the availability of this tool will also accelerate the development of genomics infrastructure in Africa. Beyond the array, we believe that having genomic infrastructure in Africa will enable further downstream studies and research to understand genomic/environmental interactions in epidemiology.
EE: How do Illumina and H3Africa hope the array will be used?
JC: The H3Africa consortium and Illumina intend for this tool to be used to study genetic factors that play a role in disease susceptibility and drug response. While genome-wide association studies have been pursued across many disease areas in European populations, we hope that similar studies will be undertaken using the array in African populations.
ZL: The array will also be used extensively for genotyping in current H3Africa-funded studies, and we hope that the larger scientific community will also take up the use of this tool too. H3Africa has employed great effort to harmonise phenotype collection across different studies, and our hope is that adding a unified genotyping approach to the study design will power additional discovery.
EE: What’s the ultimate goal of the technology? How could it help improve the health of a continent?
ZL: To date there is still a massive paucity of African genomic data. As we move into the precision medicine era, it is imperative that we improve the way we study the genomics of disease in African populations to ensure we have a clear understanding of the underpinning causality of disease pertinent to the continent. Building tools such as this African array is but one step towards reaching the potential long-term success of enabling the capacity for health-related genomics breakthroughs in Africa.