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African genomics stands on its own

Speed read
  • Genomic research has long neglected African populations, so H3ABioNet was established to empower African scientists. 
  • A lack of skilled human resources is chief among the challenges to genomic research in Africa.
  • Research networks require further refinement to be used for genomic analysis, however.   

There is a host of challenges facing genomics research in Africa, from a shortage of skilled human resources, to a lagging cyberinfrastructure for high-performance analysis. H3ABioNet is leading the way to a sustainable bioinformatics network in Africa.

H3ABioNet is a pan-African bioinformatics network of scientists across 32 institutions in 15 African countries, with additional nodes in the US and UK. Launched by the Human Heredity and Health in Africa (H3Africa) initiative funded by the US National Institute of Health and the Wellcome Trust, H3ABioNet is an attempt to fill the critical role of bioinformatics in African genomic research.

<strong> Nascent network.</strong> Managed from a node at the <a href='http://www.uct.ac.za'>University of Cape Town (UCT),</a> H3ABioNet has members in 17 countries around the globe. Look <a href='http://www.h3abionet.org/home/consortium'>here for an interactive map</a> showing the institution and investigator at each node in the H3ABioNet community. Courtesy Nicola Mulder.

The H3ABioNet network is operated from a central node at the University of Cape Town (UCT) in South Africa, with over 30 nodes in different African countries. There are two international partners, a node at the National Center for
 Supercomputing Applications (NCSA) at the University of Illinois in the US, and another at the Sheffield Institute for Translational Neuroscience at the University of Sheffield, UK. (Look here for a full list of the H3ABioNet team.)

“Most previous studies on human genomics have been performed on populations outside of Africa,” says Nicola Mulder, professor of Computational Biology at the UCT, and leader of the H3ABioNet team. “However, Africa is the cradle of mankind, the African populations are the origin of others, and harbor the greatest genetic diversity on earth.”

Excluding these genetic populations – as most human genome studies have to date – leaves huge gaps in our understanding.

“With the highest burden of disease, Africa is also rich in potential samples with interesting phenotypes to unravel the genetic and environmental basis for both communicable and non-communicable diseases. Due to the large genetic diversity in Africa, therapeutics designed for populations of European descent are often not effective in the African setting,” Mulder says.

High marks and hi-tech hurdles

H3ABioNet has helped establish bioinformatics facilities in Egypt, Mali, Morocco, Ghana and elsewhere, and has increased institutional computing capacity across the continent. A total of 15 servers with 512 cores, 2,384 GB RAM, and 120 TB of storage have been implemented in the last two years, and over 450 people have been trained to administer and further train others to use this developing cyber-infrastructure.

At least two universities have started new bioinformatics degree programs modeled after a H3ABioNet degree development curriculum. The last few years have also seen the first MSc graduates in bioinformatics.

The technical challenges hamstringing pan-African genomic research are formidable, however. Well-trained scientists familiar with the latest technology and techniques are in short supply in Africa. These few scientists juggle teaching responsibilities and struggle for research funding.

Transferring data is also a difficult challenge in an environment with unreliable electricity and internet connectivity.  Perhaps the pan-African connection proposed by AfricaConnect2 will help solve this problem.

But even under the best levels of connectivity, transferring genomic data can be a challenge.

“One lesson we’ve learned is that having large data pipes serving academic institutions all over the world is very nice on paper,” says C. Victor Jongeneel, director of the high-performance biological computing group at the University of Illinois, and member of the H3ABioNet team.   “But they’re totally useless if you don’t also have standards for how these pipelines are connected to campus-level networks, and how the protocols work that move data across these pipelines.”

His team has helped H3ABionet set up standards of operation and node accreditation procedures, and has helped to train interns to use the high-performance environment at NCSA.

Jongeneel says that even though the amounts of data are not that daunting (a few hundred terabytes), having to navigate campus and unit level firewalls and the need for standardized data endpoints creates barriers that complicate what appears to be a simple data packet transfer.

“The lesson is that we are still very far away from the situation where these wonderful research networks can actually be used for research,” Jongeneel says, and points to a Science DMZ such as they have implemented at NCSA as a solution to this bottleneck. These DMZs offer an optimized network environment for scientific efficiency, including adapting security protocols for  high volume data transfers.

Toward an ethical future

“We absolutely have to break the paradigm where African labs are used only for data collection,” says Jongeneel. “What the H3ABionet is trying to do is to empower African scientists to do data analysis themselves.”

<strong>Home field advantage. </strong> Due to the large genetic diversity in Africa, therapeutics designed for populations of European descent are often not effective in the African setting. H3ABioNet is fostering a network of scientists to study and develop precision medicines for the African population.The typical model has been for well-intentioned Westerners to bankroll African genomic research projects. But once local samples are collected, they are shipped overseas and the African scientists never see them again. “There is something wrong with that picture. African scientists are used purely as instruments to do sample collection, and they have to be able to stand on their own two feet scientifically,” Jongeneel says.

Solving these challenges won’t be an easy task, but Mulder maintains an optimistic view of the future of African genomic research. “In 10 years time there should be a number of strong bioinformatics teams who are capable of taking data from the machine to interpretation. I hope that consortia like H3Africa will continue to bring researchers together to share their experiences and work towards the common goal of building research capacity. Scientists should be focusing on translational research and driving the development of new therapies relevant to African populations. It is my that hope African genomic research will be thriving.” 

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