H3ABioNet, a pan African bioinformatics network for H3Africa, had the enormous task of building bioinformatics capacity for genomics research against a backdrop of high disease burden, limited resources, poor internet and a large gap in bioinformatics skills in Africa. Despite these challenges, the network achieved a number of successes by building computing infrastructure and associated skills, developing and facilitating access to analysis tools, and implementing a comprehensive training programme. In the next phase, H3ABioNet will extend these activities more broadly to develop a robust and innovative informatics network that addresses the complex needs of genomics researchers from clinical and biological data collection to genomic data generation and analysis and ultimately to impactful translation health research. The network will be the H3Africa data coordinating centre, hosting the data prior to submission to public repositories and providing access to data in line with the needs and consent of PIs and participants. It will ensure that data is quality controlled, standardized and interoperable. In order to facilitate adequate exploitation of genomic data, H3ABioNet will improve the user experience with genomics tools, adapting them, where necessary, for African data. The network will also go beyond this by seeking innovative data integration and translational solutions to enable comprehensive systems level analysis of diseases to ensure African scientists not only remain internationally competitive, but lead the way in translational research with tangible benefits for patients. The informatics infrastructure will be implemented through eight work packages: 1) Health Informatics; 2) Data and standards; 3) Databases and resources; 4) Pipelines and Computing; 5) Tool Development; 6) Integration; 7) Training; and 8) Sustainability, Outreach and Development. A ninth, cross-cutting activity, will be H3Africa project and Coordinating Center support in data analysis and the use of the infrastructure developed. H3ABioNet will reach out to all members of the H3Africa consortium and beyond to ensure maximum utilization of our resources and to transfer skills across the continent. It will develop the next generation of African scientists who have multidisciplinary skills and the capacity to successfully attract research funding. Links with national and international organisations and networks will ensure that these scientists remain on the cutting edge of genomics and are well placed for future realisation of precision medicine.

Public Health Relevance

H3ABioNet will implement an innovative informatics network for H3Africa and develop long- term capacity in bioinformatics and genomics by establishing and facilitating access to a robust infrastructure and developing the next generation of multidisciplinary African researchers. The infrastructure will provide the genomics tools and skills necessary to unravel the complexity of diseases that are influenced by both genetics and environment, often unique to the African setting. This will enable African scientists to take ownership of their data and its exploitation to translate their research findings into tangible health benefits to patients.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Resource-Related Research Projects--Cooperative Agreements (U24)
Project #
5U24HG006941-08
Application #
9749216
Study Section
Special Emphasis Panel (ZHG1)
Program Officer
Wiley, Kenneth L
Project Start
2012-08-15
Project End
2022-06-30
Budget Start
2019-07-01
Budget End
2020-06-30
Support Year
8
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of Cape Town
Department
Type
DUNS #
568227214
City
Rondebosch
State
Country
South Africa
Zip Code
7700
Brown, David K; Tastan Bishop, Özlem (2018) HUMA: A platform for the analysis of genetic variation in humans. Hum Mutat 39:40-51
Mulder, Nicola; Abimiku, Alash'le; Adebamowo, Sally N et al. (2018) H3Africa: current perspectives. Pharmgenomics Pers Med 11:59-66
Lemoine, F; Domelevo Entfellner, J-B; Wilkinson, E et al. (2018) Renewing Felsenstein's phylogenetic bootstrap in the era of big data. Nature 556:452-456
Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D et al. (2018) The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput Biol 14:e1005772
Gurwitz, Kim T; Aron, Shaun; Panji, Sumir et al. (2017) Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience. PLoS Comput Biol 13:e1005715
Brown, David K; Penkler, David L; Sheik Amamuddy, Olivier et al. (2017) MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics 33:2768-2771
Choudhury, Ananyo; Ramsay, Michèle; Hazelhurst, Scott et al. (2017) Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nat Commun 8:2062
Nkya, Siana; Mgaya, Josephine; Urio, Florence et al. (2017) Fetal Hemoglobin is Associated with Peripheral Oxygen Saturation in Sickle Cell Disease in Tanzania. EBioMedicine 23:146-149
Mugo, Jacquiline W; Geza, Ephifania; Defo, Joel et al. (2017) A multi-scenario genome-wide medical population genetics simulation framework. Bioinformatics 33:2995-3002
Unver, Turgay; Wu, Zhangyan; Sterck, Lieven et al. (2017) Genome of wild olive and the evolution of oil biosynthesis. Proc Natl Acad Sci U S A 114:E9413-E9422

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