H3Africa Informatics Network

H3ABioNet

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

Funding

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

H3ABioNet

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
August 18, 2020

African Collaborative Center for Microbiome and Genomics Research (ACCME)

The African Collaborative Center for Microbiome and Genomics Research (ACCME) leverages advanced research methods, technologies and international partnerships to engage African scientists
August 4, 2020

Africa Wits-INDEPTH Partnership for Genomic Research (AWI-Gen)

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 16, 2018

AWI-GEN 2: Genomic and Environmental Risk Factors for Cardiometabolic Disease in Africans

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
April 4, 2018

African Collaborative Center for Microbiome and Genomics Research (ACCME)

The African Collaborative Center for Microbiome and Genomics Research (ACCME) leverages advanced research methods, technologies and international partnerships to engage African scientists
April 4, 2018

Burden, spectrum and etiology of type 2 diabetes in sub-Saharan Africa

Our primary aim is to assess the burden and aetiological characteristics of T2D in adults in SSA using large scale population based approaches. To achieve this, we aim to develop a large scale epidemiological and genomic research resource comprising up to 12,000 cases of T2D and a population based cross-sectional study of up to 12,000 participants drawn from diverse sampling frames across SSA. Scientific objectives:
April 4, 2018

TrypanoGEN: An integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasis

The over-arching aim of this network is to improve the health of people living in some of the poorest countries in the world that carry a disproportionate burden of infectious diseases. Despite their importance, the study of many tropical diseases has lagged behind that of diseases of developed countries.
April 4, 2018

The RHDGen Network: Genetics of rheumatic heart disease and molecular epidemiology of Streptococcus pyogenes pharyngitis

Rheumatic heart disease (RHD) results from a harmful response of the immune system to a bacterium called Streptococcus pyogenes or Group A Streptococcus (GAS). Although the development of RHD can be prevented by the treatment of GAS infection with penicillin, this has not been successful in