H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

[1]  Andre Franke,et al.  Genome-wide association study indicates two novel resistance loci for severe malaria , 2012, Nature.

[2]  E. Zeggini,et al.  The African Genome Variation Project shapes medical genetics in Africa , 2014, Nature.

[3]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[4]  Life Technologies,et al.  A map of human genome variation from population-scale sequencing , 2011 .

[5]  Francisco M. De La Vega,et al.  Genomics for the world , 2011, Nature.

[6]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[7]  A. Morris,et al.  Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2 , 2010, Nature Genetics.

[8]  A. Price,et al.  Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. , 2014, Human molecular genetics.

[9]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[10]  Scott M. Williams,et al.  Genetic studies of African populations: an overview on disease susceptibility and response to vaccines and therapeutics , 2008, Human Genetics.

[11]  M. McCarthy,et al.  Research Capacity: Enabling African Scientists to Engage Fully in the Genomic Revolution , 2014 .

[12]  Celia W. G. van Gelder,et al.  GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training , 2015, PLoS Comput. Biol..

[13]  Ian T. Foster,et al.  Globus Online: Accelerating and Democratizing Science through Cloud-Based Services , 2011, IEEE Internet Computing.

[14]  K. Lobb,et al.  Analysis of non-peptidic compounds as potential malarial inhibitors against Plasmodial cysteine proteases via integrated virtual screening workflow , 2016, Journal of biomolecular structure & dynamics.

[15]  Faisal M. Fadlelmola,et al.  Enabling Genomic Revolution in Africa , 2019, The Genetics of African Populations in Health and Disease.

[16]  C. Tyler-Smith,et al.  Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. , 2012, American journal of human genetics.

[17]  Michèle Ramsay,et al.  Africa: the next frontier for human disease gene discovery? , 2011, Human molecular genetics.

[18]  David K. Brown,et al.  JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing , 2015, PloS one.

[19]  J. Casanova,et al.  An autosomal dominant major gene confers predisposition to pulmonary tuberculosis in adults , 2006, The Journal of experimental medicine.

[20]  Shaneka S. Simmons,et al.  Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes , 2014, Microbiology insights.

[21]  C. Rotimi,et al.  Ancestry and disease in the age of genomic medicine. , 2010, The New England journal of medicine.

[22]  Mattias Jakobsson,et al.  Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History , 2012, Science.

[23]  Peter Donnelly,et al.  Genome-wide and fine-resolution association analysis of malaria in West Africa , 2009, Nature Genetics.

[24]  A. Wonkam,et al.  Ethics of human genetic studies in sub-saharan Africa: the case of Cameroon through a bibliometric analysis. , 2011, Developing world bioethics.

[25]  M. Pepper,et al.  Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa , 2012, Journal of Medical Ethics.

[26]  Nicola J. Mulder,et al.  Bioinformatics Education—Perspectives and Challenges out of Africa , 2014, Briefings Bioinform..

[27]  Kenneth K. Kidd,et al.  Hunter-gatherer genomic diversity suggests a southern African origin for modern humans , 2011, Proceedings of the National Academy of Sciences.

[28]  Tom H. Pringle,et al.  Complete Khoisan and Bantu genomes from southern Africa , 2010, Nature.