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After Year of Scaling Up, Africa's 54gene Seeks Research Projects, Pharma Partnerships

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NEW YORK – With 100,000 Africans now covered by its biobank, a suite of Illumina instruments at its disposal, and plenty of cash from a recent financing round, African health technology company 54gene is eager for partnerships with researchers and biopharmaceutical companies alike.

"We have hit a milestone in terms of participant recruitment," said Abasi Ene-Obong, founder and CEO of the firm, which maintains offices in Lagos, Nigeria, London, and Washington, DC. "Our initial milestone was to get 100,000 participants," he said. "Now we are looking at how we can expand our studies in multiple geographies to triple or quadruple that number within the next 18 to 24 months."

With that number of samples banked, together with complementary phenotype and clinical data, 54gene is also ready to begin generating genomic data, Ene-Obong said. "We are really looking forward to the next 12 months," he said. "We have brought on teams to help with the science, particularly going into drug discovery. That is something we are commencing as a company."

Ene-Obong founded 54gene three years ago to fill a gap in the generation of data relevant to Africans, as well as use that knowledge to improve healthcare. "In the field of population genetics, which is really beginning to transform healthcare, how could you have a population of 1.2 billion people, with 2,000 different ethnic groups, that nobody has really studied?" said Ene-Obong.

His vision for 54gene also matched with similar projects across Europe and North America to gather genomic and clinical data to improve the health of local populations, the UK Biobank among the most prominent. "I thought it was the right opportunity to go after," said Ene-Obong, "an opportunity that was manifold in that it can provide insights that will transform biology for Africans and non-Africans alike, and in so doing build up infrastructural gaps on the African continent and give people access to skilled jobs while training them in the process."

The company closed a series A round worth $15 million last year and currently employs close to 100 people across three offices. In April 2020, the company also set up a scientific advisory board, while building out its lab in Lagos to support the sequencing and genotyping of its growing wealth of samples. 54gene has also acquired several of Illumina's higher end instruments, including the NovaSeq 6000 and NextSeq 550Dx. It also has an iScan system for array-based genotyping.

According to Ene-Obong, 54gene is one of two facilities in Africa that has the NovaSeq 6000, the other being the African Center of Excellence for Genomics of Infectious Diseases, a World Bank-funded research organization. As such, 54gene is the only private institution to have the instrument, which Illumina rolled out three years ago.

"It's been a good collaboration," said Ene-Obong of 54gene's relationship with the San Diego vendor. "I think they really want to open up the market."

Complementary technologies

Whole-genome and whole-exome sequencing and array-based genotyping are therefore at the firm's disposal. Colm O'Dushlane, vice president of genomics and data science at 54gene, said that the company views these as "complementary technologies'' that will support its mission.

"Sequencing will help us identify rare and potentially pathogenic variations, novel to African populations, at genes of interest such as existing therapeutic targets or known candidate disease-associated loci," said O'Dushlane. "This will help inform on why these therapeutics sometimes have unpredictable results in African individuals."

It will also help to better characterize the landscape of modifiers of drug response and disease severity, key goals of 54gene's research, he said. To complement sequencing, lower-cost array-based genotyping will allow 54gene to perform analyses across all traits in its biobank, and to run association scans using much larger sample sizes, he said. The researchers will also use the sequenced individuals as a reference for imputing genotyped variants to increase the number of variants available for analysis.

"Together, these approaches will help yield better insights into variants influencing disease in African populations and drive the identification of novel therapeutic targets that may ultimately help all populations," said O'Dushlane.

COVID-19 mobile labs

Like many tech companies around the world, when the COVID-19 pandemic hit, 54gene partnered with the local government, in this case Nigeria's, to provide resources for testing. "We worked with the government to upskill them to run molecular diagnostic tests," noted Ene-Obong.

When COVID-19 hit, there were about half a dozen public labs capable of providing tests to the West African nation's population of 207 million, the seventh largest in the world. "The capacity at the beginning of the pandemic was somewhere around 200 tests per day," noted Ene-Obong.

Since it began offering real-time PCR testing for COVID-19, 54gene has processed around 100,000 tests, he said. There have been close to 100,000 confirmed cases in Nigeria since the pandemic began, and about 1,300 deaths. Still, Ene-Obong noted, the number of infected individuals is likely higher. "In Nigeria, there haven't been many tests done," he said.

To improve detection of the disease, 54gene developed mobile labs that could be deployed to locations with high need. It usually takes about a week to 10 days to assemble a lab and begin testing, and 54gene dispatches specialized teams to set up and operate the mobile labs, he said.

Things to come

While COVID-19 testing continued unabated, 54gene is looking to run more studies with African partners in 2021, in part to build out its biobank, which already contains samples from more than 300 populations. The company typically gains access to new samples via such studies which focus on a variety of indications, including cancer and rare diseases. Ene-Obong declined to name partners at this time.

This year, however, will see some academic papers published that highlight this work. The company is also engaging academics and medical professionals in Africa so that they can better interact with 54gene and contribute to each other's projects. The company is equally open to partnerships with biopharmas.

"There is a lot of interest around what we are building," he said. "We have had serious conversations with every serious company doing drug discovery."

When asked what the next milestone will be for the biobank, Ene-Obong said there is a limit to how big any resource can grow, but that the main question is how sustainable it is to grow it.

"One thing we are looking at going into 2021 is expanding our model for partnership, especially around building cohort sizes and that is going to be very interesting with some of the things we have planned," said Ene-Obong. "Yes, we could build this to millions, but how [do we] do it sustainably so we are not just throwing money at building a biobank or making sure there is scientific value coming out of it, economic value coming out of it, and most important value to patients coming out of it?" he said. "Still, Africa has a population of 1.2 billion people," he added. "We haven't even scratched the surface of what is possible."

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