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H3Africa/H3ABioNet Case Study/Nicola Mulder


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Presented during the AOSP high-level meeting on 3-4 Sept. 2018, Pretoria, South Africa.

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H3Africa/H3ABioNet Case Study/Nicola Mulder

  1. 1. H3Africa/H3ABioNet case study Prof Nicola Mulder H3ABioNet PI Head of Computational Biology University of Cape Town
  2. 2. Outline • What are H3Africa & H3ABioNet? • Role of H3ABioNet • H3Africa/H3ABioNet policies and governance • Successes • What worked and what didn’t
  3. 3. H3Africa: Human Heredity & Health in Africa • H3frica Vision: “To facilitate an Africa-based contemporary research approach to the study of genomics and environmental determinants of common diseases with the goal of improving the health of African populations” • Building the infrastructure for genomics research • Funding: NIH, Wellcome Trust/Alliance for Accelerating Excellence in Science in Africa AESA
  4. 4. H3Africa in Numbers >$170 million of funding 48 research projects 29 African countries >500 investigators >75,000 research participants >130 publications 139 trainees/study coordinators supported 53 workshops/courses
  5. 5. H3Africa in Numbers >$170 million of funding 48 research projects 29 African countries >500 investigators >75,000 research participants >130 publications 139 trainees/study coordinators supported 53 workshops/courses Phenotype data Genomic data ~1 PB
  6. 6. The H3Africa Consortium 14 Collaborative Centers 13 Research Projects 3 Pilot Biorepositories 8 Ethics Grants The H3Africa Consortium Bioinformatics Network 4 Global Health Bioinformatics Training Programs H3ABioNet
  7. 7. H3ABioNet: Informatics network • H3ABioNet is a Pan African Informatics Network, to provide bioinformatics infrastructure and support for the H3Africa consortium • Aims: • To implement a Pan African informatics infrastructure • To develop an H3Africa data coordinating center • To provide high quality informatics support to H3Africa • To enable and enhance innovative translational research • To address outreach, development and sustainability 28 partners in 17 countries:
  8. 8. Role of H3ABioNet • H3ABioNet supports H3Africa research projects by: • Building relevant skills for data analysis and interpretation • Ensuring access to the computing infrastructure for moving, storing and analysing data • Developing containerized workflows to make data analysis easy, consistent and reproducible • Providing support for data analysis using existing or developing new algorithms • Preparing their data for submission to the EGA/ENA • Ensuring data is FAIR, promoting open science (panels, WGs) • For the H3Africa consortium H3ABioNet has: • Developed a participant recruitment database • Developed a trainer/trainee tracking database • Worked with the PHWG to harmonize H3Africa data, map it to ontologies and make it FAIR • Developed an H3Africa catalogue to enable searching of the H3Africa data and biospecimens for the public to request access Aim is to enable genomics research in Africa
  9. 9. H3Africa governance • All funding applications required letter of support from institution and government • All projects are governed by contracts with the funders and funder policies • Close cooperation of funders with steering committee • Set up H3Africa Coordinating Centre and now also secretariat at AESA • Biannual H3Africa consortium meetings • H3Africa working groups for specific issues
  10. 10. H3Africa management structure
  11. 11. H3Africa management structure Consortium members Affiliate members
  12. 12. H3Africa management structure Administration & Communication, M & E, Training Resources, opportunities & Tracking of Trainees Hub and spoke model of nodes General Assembly Management Committee Scientific Advisory Board Manage access to data and biospecimens
  13. 13. H3Africa consortium organization Steering Committee Chair/Co Chair PIs, NIH/AESA/Wellcome H3ACC BioR PIDSAR Ethics & Regulatory Community Engagement Genome Analysis Phenotype Harmonizat ion Sustainability HIV Publica tions CVD Independent Expert Committee Working Groups
  14. 14. H3Africa Policies & Guidelines 1. H3Africa Guidelines for Community Engagement 2. H3Africa Publications Policy 3. H3Africa Guidelines for Informed Consent 4. Framework for African Genomics and Biobanking 5. H3Africa Phenotype Harmonization Working Group Recommendations 6. H3Africa Data Sharing, Access & Release Policy, 7. H3Africa Data and Biospecimen Access Committee Guidelines 8. H3Africa Biorepository Submission Documents
  15. 15. Successes • Value of network/consortium is greater than sum of its parts • >130 individual and joint publications • Inclusive and comprehensive policies and guidelines developed • Data is being harmonized and made available via: • EGA, ENA • H3Africa catalogue • Meta analysis has been performed as a consortium effort –about to be published • Very successful training program –based on demand, enabled by funding and creative methods • Built critical mass locally and regionally • Pushed for open sharing of training materials, code, etc • Efficient monitoring of specific metrics and general progress
  16. 16. What worked • Having clear policies from funders in contracts & close cooperation • Strong focus on building capacity and infrastructure: biorepositories, bioinformatics, research • Good training program –coordination of courses, fellows program • Regular face-to-face meetings, focussed jamborees/hackathons • Joining forces to solve common problems –community efforts • Having common goals, and preferably also incentives • Collaboration between related projects for data harmonization • Working with relevant outside expert bodies (Globus, NRENs, EGA, GOBLET, etc) • Inclusivity and transparency • Need for future sustainability –have to perform well! Sustainability WG and activities at consortium meetings • Incentives: Funding is a big incentive! Others include publication and recognition
  17. 17. What didn’t work/challenges • Not yet buy in from everyone –some individuals work alone • The need for data harmonization and sharing is still not completely recognized by PIs • Still a sense of protection of data • Harmonized data collection is not universal across projects • Data is slow to be released • Long term sustainability is an issue • General challenges: • High demand for infrastructure & skills • Funding across countries • Travel around Africa
  18. 18. Acknowledgements The H3ABioNet & H3Africa Consortium Funding: NIH Common Fund, NGHRI grant: U41HG006941, U24HG006941 H3ABioNet team at CBIO: • Sumir Panji • Gerrit Botha • Ayton Meintjes • Suresh Maslamoney • Ziyaad Parker • Kim Gurwitz • Mamana Mbiyavanga • Katherine Johnston • Paballo Chauke • Verena Ras