Skip to main content
Premium Trial:

Request an Annual Quote

Spurred by H3Africa Consortium, Illumina Introducing Array to Close Population Gaps in Future GWAS


NEW YORK (GenomeWeb) – Illumina has announced the upcoming availability of a new genotyping tool that it developed in collaboration with the Human Heredity and Health in Africa (H3Africa) Initiative.

Both the company and the consortium hope the array will allow future GWAS to address African genomic diversity in a way that previous chips have not, leading to discoveries that can improve the health of both African peoples and the broader global population.

The development of genomic tools that specifically address non-European populations has lagged sorely, with the result that the genomic diversity of certain populations is much less well-understood than that of the European peoples who have been studied the longest and most extensively.

This means that our ability to understand what certain variants mean, even in European populations, is handicapped by an overall lack of data on the full diversity of human genomes. Researchers from the University of Washington, for example, highlighted in a study last year that ethnic disparities in genomic data mean that calling variants as pathogenic or not can be difficult across the board. Variants seen only rarely in one population may turn out to be common in another, meaning they probably don't cause disease, but this may not be clear without pan-ethnic data.

Although there has been growing recognition of this unmet need, researchers interested in doing studies that can fill population-specific genomic gaps need cost-effective tools to support them.

Julie Collens, senior manager of market development at Illumina, told GenomeWeb this week that this was the driving goal for the Wellcome Trust- and National Institutes of Health-funded H3Africa initiative in setting out to create a continent-specific array.

The question of whether such a tool would be needed came up from the inception of the consortium a few years ago. Once the group decided they did need a new genotyping tool, it reached out to several biotech companies, Collens said, and eventually decided to work with Illumina to create the array.

Developing tools that can help fill gaps in global human genome research is an independent goal of Illumina's, Collens added, so the company was excited to become part of this development effort.

"From Illumina's point of view, we have a drive to unlock the power of the genome not just in North America or in European populations, but globally," she explained.

"Absolutely [the company] understands that there is a need for this … [because] genetic risk really does matter based on your background, so not having something that is specific … especially in terms of variation across a continent as large as Africa, really requires addressing," she said.

According to Collens, the new chip borrows significantly from Illumina's Infinium Multi-Ethnic Global BeadChip (also called the Multi-Ethnic Global array, or MEGA), which was developed with collaborators from several consortia and is also aimed at increasing the representation of populations across the globe in genotyping efforts.

Although it shares a backbone of content with MEGA, the new H3Africa array incorporates a variety of unique content developed and supplied to Illumina by the H3Africa consortium researchers.

"Their process was basically to do sample collections that represented different linguistic groups within Africa, then … whole-genome sequencing to allow them to identify variations unique to those populations," Collens said.

As part of the chip development, for example, researchers from the University of Illinois at Urbana-Champaign and the University of Cape Town worked together using supercomputing to identify genomic variants in over 300 deeply sequenced human samples, with the goal of coming up with a list of genomic variants for the new chip.

Zané Lombard, co-chair of H3Africa's genome analysis working group, said in a statement that the consortium believes the new chip will help researchers study the environmental and genetic factors that play a role in disease susceptibility and drug responses.

Amongst the projects the consortium is tackling that the new array could play a role in are studies of the genetic contributions to diseases like rheumatic heart disease, diabetes, neurological disorders, and individual responses to anti-tuberculosis drugs.

Researchers outside of the H3Africa initiative can and hopefully will also start using the array, said Collens.

"The consortium is extremely motivated to have this in as many hands as possible," she said. "Having the tool available really drives the infrastructure part forward for the consortium … but [there is also recognition that] the power of the data is stronger if you have more people involved."

Illumina did not provide details on the exact timing of the new array's commercial availability.

While the new H3Africa array is unique, Illumina has competition for some of its other products in this vein.

For example, Thermo Fisher Scientific announced earlier this year the availability of its new Axiom Precision Medicine Research Array, which it hopes can play a major role in accelerating and supporting global precision medicine initiatives.

The new Thermo Fisher chip is aimed at global screening programs in diverse populations, much like Illumina's Global Screening Array (GSA), which allows researchers to genotype samples across 660,000 markers.