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Africa Genomics Effort Taking Shape

By Matt Jones

NEW YORK (GenomeWeb News) – A new international effort will seek to expand and enhance the capabilities for using genomics in Africa by creating new infrastructure, investing in training, and funding specific genomics and bioinformatics research projects.

A partnership between the National Institutes of Health, the Wellcome Trust, and the African Society of Human Genetics (AfSHG),The Human Heredity and Health in Africa (H3Africa) project will aim to catalyze and enable human genomics-based science in Africa, of particular interest to Africans, and conducted by African researchers, according to a new white paper proposal for the project.

The goal of the project is to establish "a viable, productive clinical and research infrastructure" by creating a network based around centers in hubs and regional nodes that branch out into the country, according to the authors of the white paper, which included scientists in Africa, Europe, and the US.

As GenomeWeb Daily News reported when the initial plans for H3Africa were released, NIH has committed $5 million per year for five years, and the Wellcome Trust has committed at least $12 million over the term of the project.

More than simply enhancing research into certain disease areas, the H3Africa project was designed to "improve the capabilities for doing research in Africa," Mark Guyer, director of NIH's Division of Extramural Research and acting deputy director of the National Human Genome Research Institute, told GWDN today.

"To the extent possible we are trying to develop what is essentially an Afrocentric plan, where the ideas, the identification of the issues, will all come from the African scientific community. The awards when they are made will be made directly to African scientists and institutions, and they will be the driving force," Guyer said.

The H3Africa project will develop four central resources, including a biorepository, regional centers of excellence, a network of clinical centers, and a bioinformatics network.

These resources will support a range of research efforts, including but not limited to clinical phenotyping; sample collection and biobanking; genotyping and gene sequencing projects; bioinformatics; statistics; functional analyses; and ethical, legal, and social issues research.

The current resources available in Africa presents unique challenges for accessing samples for disease and biology research, so this program will require the creation of biorepositories for the storage, retrieval, distribution, and management of large sample collections. The efforts also will require technological infrastructure units, including centers for genetic and genomic data generation and analysis.

The biorepository resource will house all of the biological specimens collected under the entire H3Africa research umbrella, and it will ensure that these samples remain in Africa and are used in collaborations to support the goals of the project.

The regional centers of excellence, which will be located along spokes radiating out from the regional hubs, will serve as core training facilities for African scientists and will house genotyping, sequencing, and phenotyping labs. This proposal is designed to "facilitate more communication between and among African Scientists and research institutions," Guyer said.

The primary collaborations that most African scientists have are outside of Africa – in the US, Europe, etc. The goal of the network approach is to try to encourage more collaboration within Africa," he told GWDN.

The program also will support a network of clinical centers, which will collect demographic, epidemiologic, and clinical data on all H3Africa participants, and they will develop standard operating procedures that will be used for patient enrollment and examination.

Another part of the program will develop a pan-African bioinformatics network that will provide a foundation for the large-scale genomic data sets that the project will generate and will be used to train scientists in bioinformatics.

Genomics-based technologies in particular may have unique capabilities in Africa, which deals with more tropical viral-based diseases than much of the rest of the world, but they also offer "the same possibilities that they offer anywhere else," Guyer explained.

"It's going to be important that progress be made on understanding disease in Africa because one cannot assume that what you learn about disease studying European or Asian or any other populations will necessarily be applicable to Africa," he said. "And it's also true that there is a large genetic ancestry there for a significant fraction of the US population, so studies there could be revealing for health issues here."

The Wellcome Trust and NIH plan to review the white paper plan at a conference in Cape Town in April, and to issue grants in the summer of 2011 that will be awarded by summer 2012, according to Guyer.

He said that for NIH the clearest "success of the program will be evidence that the people who are supported under this program become competitive for independent funding for genomic science, and are either competing for NIH grants or grants elsewhere.

"Since the goal is to help develop the capability, the measure will be their ability to attract independent research funding, publish papers, and so on," he added.

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