New Genetic Chip A Step Toward Diversity In African Genome Sequencing

Avatar
Written by Dana Sanchez

Africa is uncharted territory when it comes to sequencing genomes and studying genetic causes for diseases that affect Africans disproportionately, but a new genetic chip is a step forward for medicine on the continent, Quartz reported.

The genetic chip project has been an Africa-led effort from the start, said Nicola Mulder, a bio-informatician at the University of Cape Town in South Africa who led the work.

However, parts of the project have been conducted in the U.S. and Europe because African countries don’t yet have the equipment to sequence entire human genomes fast, Quartz reported. Some of the work was done at Baylor College of Medicine in the U.S.

“This will be the first chip that has been created to specifically target genetic variation in African populations and people of African descent,” Mulder said, according to Quartz.

Precision medicine — scanning patients’ genes to create tailor-made treatment programs—is routine for some diseases in affluent countries. Oncologists in the U.S. and Europe use genetic tests to decide which treatments will work best for their patients’ cancers.

But Africans and African descendants including African Americans were left behind. Out of the 35 million-plus people who have participated in genetic screening studies, 81 percent were of European ancestry. Three quarters of the rest were Asians. Just 3 percent were of African origin.

San Diego-based Illumina, Inc. announced in October that it is creating an African array for genome-wide association studies by the Human Heredity and Health in Africa (H3Africa) Initiative. The array will include 2.5 million variations of specific interest to African populations, Bio IT World reported.

Illumina manufactures integrated systems for analyzing genetic variation and biological function. In 2016, Illumina ranked No. 3 on MIT Technology Review‘s list of 50 smartest companies.

Illumina’s customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies. Its tools provide researchers with the ability to perform genetic tests needed to extract medical information.

Based in Bethesda, Maryland, U.S.A., the H3Africa initiative is a partnership between the U.S.-based National Institutes of Health, the African Society of Human Genetics, and Wellcome Trust, a U.K.-based biomedical research charity.

The initiative has already done whole genome sequencing on about 3,000 Africans, said Julie Collens, senior manager of market development at Illumina, according to Bio IT World.

“One of the goals of the consortium is to be able to bring infrastructure and genetic studies to Africa,” Collens said.

“We are actively working now on the design of the chip … we expect to begin shipping the chip early (in 2017).”

Research into genetic health risk factors for Africans is challenging for several reasons. People of African descent are greatly underrepresented in genomics databases so far. Plus the degree of diversity in African samples is greater than any other region on Earth.

Without information, researchers may be missing key genetic factors that play a role in disease susceptibility and drug response among different population groups, according to MIT Technology Review.

“They’ve discovered something like 100 million or more variants that are specific to African populations,” Collens said, according to Bio IT World. 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.”

Scientists hope that Africa’s as-yet uncharted genetic variations can help explain why people on the continent are more susceptible to certain conditions.

The research community assumed that poorer countries, like many in Africa, don’t need genomic studies because the biggest killers there are infectious diseases, said Adebowale Adeyemo, a director at the NIH.

But chronic diseases like diabetes and heart disease are now rising in lower-income countries too. More genome studies are needed to understand different populations’ risks, he said, according to MIT Technology Review.

For example, Africans develop chronic kidney disease about 20 years earlier than Europeans, Quartz reported. “It’s a complete nightmare illness,” says Adu Dwomoa, a Ghana-based researcher in charge of a multi-country study looking for genetic clues as to why the disease hits Africans so young. The disease affects up to 40 percent of sub-Saharan African adults, he says. Few have access to expensive dialysis treatment, and so they die. Dwomoa hopes his research will lead to new treatments that work in Africa.

The chip is a step in the right direction, but it still won’t represent all the diversity in African populations, Collens said. H3Africa believes the new array will encourage genomic and epidemiological research and improve the health of Africans.

“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, according to Bio IT World. It’s a cost-effective way to begin addressing health disparities.

H3Africa wants grant applicants for related research to incorporate its array in their studies. The community hopes that a standardized research platform will power additional discovery.

“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.”

Understanding the genetics of African people is imperative, said Charles Rotimi, a Nigerian geneticist who works for the U.S. National Institutes of Health. “Without it you can’t tell the story of the rest of the world,” he said.

The benefits should be felt beyond the continent, Mulder said. Since humankind originated in Africa, its genetics charts the history of all of humanity.