H3Africa Informatics Network


The Goal: to develop bioinformatics capacity in Africa through training and support for data analysis, while also facilitating access to informatics infrastructure in the form of pipelines and tools for human, microbiome, and pathogen genomic data analysis.

Project Leads

Prof. Nicola Mulder

University of Cape Town

The Problem

Researchers working in the life sciences are generating data of increasing size and complexity due to modern research techniques. Interpreting this data is essential for understanding health and disease and developing solutions to improve African and global health. Considering this and also the lack of modern research infrastructure in Africa, there is an ever-increasing need to develop the human and physical capacity for bioinformatic research in Africa to enable the interpretation of valuable African genomics data.

Project Strategy

  1. Implement a pan-African informatics infrastructure
  2. Develop an H3Africa Data Coordinating Center
  3. Provide high quality informatics support to H3Africa
  4. Enable and enhance innovative translational research
  5. Establish outreach and sustainability plans

Outcomes to Date

Training and Development
• 40 Courses/workshops run, 29 face-to face, 2,256 people trained
• Annual introductory and intermediate online courses
• New bioinformatics degree programs developed in 4 African countries
• 15 accreditations in analysis of genomic data awarded

Enabling Genomic Medicine in Africa
• Designed new genotyping chip for African populations
• African genome reference panel for imputation
• Genomic medicine curriculum designed and 225 nurses trained
• Clinical data collection and phenotype harmonization support

Computing Infrastructure
• 17 computing facilities developed across 11 countries
• 3432 cores for data processing
• 1.2 petabytes available for storage and processing of African genomic data
• 4 genomic data analysis workflows developed and openly accessible

Data Management, Structure, and Transfer
• 14 African genomics datasets (135TB) stored in H3Africa archive
• 13 datasets QC’d and submitted to pubic repositories
• Created the H3Africa Data Catalogue, which allows users to search for datasets and biospecimens of interest
• 77.3 terabytes of African genomic data transferred

Project Sites

H3ABioNet is a pan-African network consisting of 28 nodes across 16 African countries.

* = Lead Institution:

South Africa: University of Cape Town

Non-African Collaborators:

USA: University of Illinois


This work is supported by the U.S. National Institutes of Health (NIH) and the National Human Genome Research Institute (NHGRI) grant number U24HG006941.


Additional Resources

H3ABioNet Website

January 29, 2021


AWI-Gen is the Africa Wits-INDEPTH partnership for Genomic Studies, an NIH funded and university supported Collaborative Center of the Human Heredity and Health in Africa
January 29, 2021

H3Africa Administrative Coordinating Center (H3ACC)

AWI-Gen is the Africa Wits-INDEPTH partnership for Genomic Studies, an NIH funded and university supported Collaborative Center of the Human Heredity and Health in Africa
January 29, 2021

Systematic Investigation of Blacks with Stroke – Genomics (SIBS-Genomics)

AWI-Gen is the Africa Wits-INDEPTH partnership for Genomic Studies, an NIH funded and university supported Collaborative Center of the Human Heredity and Health in Africa
October 8, 2020

Breast Milk Microbiota Influence on Infant Immunity and Growth (BEAMING)

Understanding microbial shifts and how they affect vaccine response is central to this study. We will determine if gut microbial communities associated with breastfeeding in the HEU infant follows the same successional trajectory as HU controls and resolve the differences at functional level. How the continuous conditioning of the infant gut by the microbiota from the breast milk affects the infant microbiome and subsequent
October 7, 2020

Intergenerational Epigenomics of Trauma and PTSD in Rwanda

The goal of the proposed work is to characterize the transgenerational genomic impact of genocide exposure and post-traumatic stress disorder (PTSD) in women survivors of the Rwandan genocide and their offspring. PTSD is a common and debilitating mental disorder that has a profound public health impact. Between April and June 1994, almost one million people died in the Rwandan genocide against ethnic Tutsi.
October 6, 2020

Transgenerational Effects of Maternal Stressors: Investigating the Role of Infant Gene Expression

This collaborative project, between Emory University in the USA and the University of Cape Town (UCT) in South Africa, proposes to investigate biological mechanisms underlying the transgenerational effects of exposure to prenatal maternal psychological stress, anxiety, or depression. We propose to examine
October 1, 2020

Immunoglobulin Gene Diversity in an African Population and Impact Antibody Function in HIV Infection

Antibodies are critical components of immune defense and are mediators of vaccine-elicited protection as well as autoimmunity. The heavy and light chains that comprise an antibody molecule are encoded by germline immunoglobulin (Ig) gene fragments that recombine and undergo somatic mutation thereby generating billions of specificities able to contend with a multitude of foreign antigens.
October 1, 2020

Nurturing Genomics and Bioinformatics Research Capacity in Africa (BRECA)

Bioinformatics is now integral to clinical and biomedical research. Without bioinformatics expertise, health research in Africa will remain suboptimal. In fact, researchers on the continent are stuck with Next Generation Sequencing data that they can barely analyze.
September 29, 2020

African Neurobiobank for Precision Stroke Medicine: ELSI Project

African Neurobiobank for Precision Stroke Medicine: ELSI Project: Project Summary Africa had, hitherto, been under-represented in the biobanking revolution. However, with the Human, Heredity and Health in Africa (H3Africa) initiative, biorepository science has been bolstered and biobanking related activities are growing on the continent