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Nigerian Research Consortium Begins Collecting Genetic, Clinical Data From 100K Subjects

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This article has been updated from a previous version to include additional information about the NCD-GHS Consortium's steering committee.

NEW YORK– A newly minted public-private research consortium in Nigeria plans to gather genomic, clinical, and other data from 100,000 citizens that will initially be used to study the genetic basis of various non-communicable diseases.

The Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) Consortium, is funded by the African Centre for Translational Genomics (ACTG), which in turn is funded by genomics research, services, and development company 54Gene. ACTG is an initiative designed to facilitate translational genomics research and precision medicine across Africa, and to invest in grant opportunities, fellowships, internships, and training for medical researchers, trainees and students.

The NCD-GHS steering committee is co-led by Babatunde Lawal Salako, director general of the Nigeria Institute of Medical Research (NIMR); Oyekanmi Nash, director of the National Biotechnology Development Agency’s Centre for Genomics Research and Innovation (NABDA-CGRI); Abasi Ene-Obong, CEO of 54gene; Segun Fatumo, assistant professor at the London School of Hygiene and Tropical Medicine (LSHTM); and Omolola Salako, consultant oncologist at the College of Medicine, University of Lagos (CMUL).

The consortium will work with senior scientists in Nigeria "that have made their mark in the field of cardiometabolic research in teaching hospitals across the country," Babatunde Lawal Salako, NIMR's director general, said in a statement. Oyekanmi Nash, director of genetics, genomics, and bioinformatics at NABDA-CGRI, noted in a statement that the consortium will also offer opportunities for the country's bioinformaticians "to build models and algorithms" that support "robust [utilization] of the genomics data."

"We all understand the value that genomics research has in helping us to further understand our health and some of the determinants of our health as well," Aminu Yakubu, 54Gene's VP of research planning and ethics, said in an interview. Prior to the NCD-GHS, all the consortium partners were already working separately toward launching similar studies, he said. Rather than duplicate efforts, it made more sense to share "our resources, our capacities, our skills, and knowledge for the betterment of the health of Nigerians."

To enroll a diverse sample of the population, 54Gene and its partners are working with large and small hospitals that are located in urban and rural parts of the six geopolitical zones in Nigeria, Yakubu explained. The consortium seeks to enroll patients with pre-diagnosed conditions of interest as well as control subjects.

The researchers will collect blood, saliva, and tissue samples from participants at each hospital site, along with phenotype information, clinical history, and lifestyle information, among other bits of information. Samples will be stored temporarily in the participating hospital before eventually being sent to 54Gene's laboratory.

The consortium plans to do whole-genome genotyping for each sample as well as sequence a subset of the samples, Yakubu said. He said that 54Gene is currently in discussions with leading suppliers of genotyping solutions to decide which will be the best fit. The company expects to have selected and implemented the genotyping technology in its laboratories by the second quarter of 2020.

For the samples that will be sequenced, the partners are currently contemplating whether to procure their own sequencing infrastructure or to outsource the job. In terms of securing and protecting patient data, 54Gene has implemented industry-standard measures including encryption capabilities and controlled data access, and samples will be deidentified.

Prior to consenting to have their data included in the study, potential research participants will receive complete information about the study as well as any risks or benefits. "We are following best practices to recruit people into our studies," Yakubu said. The consortium also works with hospitals to secure proper institutional approvals for the research, and works with partner clinicians at each site who serve as principal investigators. These clinicians will provide feedback on the proposed research protocols, and work with the consortium to ensure that the research aligns with the policies at their respective institutions. They also need approval from the ethics committees at their hospitals prior to starting the study.

Initial studies under NCD-GHS will focus on conditions such as cardiovascular disease, endocrine diseases, neurodegenerative diseases, different cancers, and sickle cell disease. The partners hope to recruit the full cohort within a year, but they plan to continue recruiting patients for as long as it takes to reach the target.

Meanwhile, the ACTG also plans to launch a second initiative focused on infectious diseases no later than the second quarter of 2020. This consortium will use data collected from the 100,000 individuals in the cohort for this second study, but will collect additional information specific to infectious diseases. Yakubu noted that the partners are currently in discussions to prioritize infectious diseases and develop study protocols, as well as secure necessary ethics approvals.

Nigerian scientists have already been involved in a number of large-scale projects aimed at cultivating genomics research in the country and on the continent. For example, the Human Heredity and Health in Africa (H3Africa) initiative has helped to improve genomic scholarship research in Nigeria and other African countries. In 2014, the National Institutes of Health awarded over $300,000 to two projects under H3Africa to study how people in Nigeria and Ethiopia understand genomics concepts and how that awareness can impact research and public health. One of these was a $162,000 grant given to researchers from Nigeria's Institute of Human Virology to study the linguistic and cultural language concepts of genomics in Nigeria and develop a participant consent form for a diabetes study.

Now with the launch of the NCD-GHS, Nigeria joins the growing list of countries with large-scale initiatives to collect genomic and clinical data from thousands of individuals for research and precision medicine. For example, in 2019, the Department of Health-Abu Dhabi launched the Genome Program to sequence samples from 100,000 individuals in the emirate in its first phase. Meanwhile, in 2017 Denmark said that it would spend DKK100 million ($14.2 million) over the next three years to implement its new National Strategy for Personalized Medicine, dubbed Per Med. Projects like these have proliferated in the wake of the UK's 100,000 Genomes Project, launched in 2012, and the US's All Of Us project, which aims to sequence the genomes of a million citizens.

Last year, 54Gene raised $4.5 million in seed funding from several investors including the Y Combinator and Fifty Years. The company, which was founded in 2019, set up shop to provide access to genetic data gleaned from diverse African populations to support the research and development of more broadly efficacious drugs and diagnostic products. It maintains offices in San Francisco and in Lagos, Nigeria.

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