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Illumina Builds Africa GWAS Chip With H3Africa Initiative


By Allison Proffitt

October 20, 2016 | Last week, Illumina announced that it is creating an array for genome-wide association studies (GWAS) by the Human Heredity and Health in Africa (H3Africa) Initiative. The array—which isn’t available yet—will be include 2.5 million variations of specific interest to African populations.  

The H3Africa initiative is a partnership between NIH, the African Society of Human Genetics, and Wellcome Trust. The initiative has already done exome and whole genome sequencing on about 3,000 individuals from across the African continent, explained Julie Collens, senior manager of market development at Illumina. From their findings, the H3Africa initiative has submitted variations to Illumina to be built into an array.

“We are actively working now on the design of the chip from that content; we expect to begin shipping the chip early [in 2017],” Collens said.

People of African descent have been woefully underrepresented in genomics databases so far, but the degree of diversity in “African” samples is also significant. Both points have made research into genetic risk factors for the health of African individuals challenging.  

“In part, the reason that they want to pursue this is because the populations and the diversity is not represented in 1000 Genomes of HapMap,” Collens said. The dataset that H3Africa collected is a sampling of genome-wide variation, including both coding and non-coding regions, representing multiple subgroups, disease areas, and populations.

“In total from the exomes and genomes, I believe they’ve discovered something like 100 million or more variants that are specific to African populations,” Collens said. The Illumina chip will represent a subset of those 100 million variants, “that basically does the best job of representing all of the different populations,” she said.

Members of the H3African consortium have contributed their own sequencing data, and submitted a superset to Illumina. Now Illumina researchers and the H3Africa researchers are working together to find the best variants to include on the chips. “The design of the content was driven entirely by the Consortium,” Collens said, but conceded that Illumina researchers are helping to identify overlap and highlight variants that perform well on the array.  

Even though the chip is a step in the right direction, it still won’t represent all of the diversity in African populations.

“One of the advantages to having one particular array that has multiple different populations or disease areas on it, is that you can find regions of overlap or you can find commonalities that are really beneficial,” Collens said. It’s a cost-effective way to begin addressing health disparities.

H3Africa believes the new array will foster genomic and epidemiological research and improve the health of people in Africa. H3Africa is hopeful that effective immediately, grant applicants for related research will consider incorporating this array in their studies. The community hopes that a standardized research platform will power additional discovery.

“A substantial and ongoing investment of resources is needed for Africans and people of African ancestry to benefit from advances in genomic and precision medicine. Investing in genomic research in Africa will benefit everyone, given that all modern humans originated in Africa 200,000 years ago,” said Adebowale Adeyemo, MD, Deputy Director of the Center for Research on Genomics and Global Health (CRGGH) at the National Human Genome Research Institute, National Institutes of Health and co-chair of the H3Africa Genome Analysis Working Group in the announcement.

“One of the goals of the consortium is to be able to bring infrastructure and genetic studies to Africa. They’re really motivated to have more data and more studies take place among African individuals specifically,” Collens said. “By having studies that address the genomics of African populations, the hope is that they benefit from the same health outcomes.”

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