the human heredity and health in africa initiative · • manjinder sandhu, wellcome trust sanger...
TRANSCRIPT
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The Human Heredity and Health in Africa Initiative 2nd H3Africa Consortium Meeting 16-18 May 2013, Accra, Ghana
Audrey Duncanson
Wellcome Trust
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TrypanoGEN – genetic determinants of susceptibility to trypanosomiasis Enock Matovu College of Veterinary Medicine Makerere University, Uganda
• Issa Sidibe, CIRDES, Burkina Faso • Dieudonne Mumba, INRB, Democratic Republic of Congo • Mathurin Koffi, University of Abob-Adjame, Côte d’Ivoire • Gustave Simo, University of Dschang, Cameroon • John Enyaru, Makerere University, Uganda • Martin Simuunza, University of Zambia, Zambia • John Chisi, University of Malawi, Malawi • Stafford Kibona, NIMR, Tanzania • Vincent Pius Alibu, Makerere University, Uganda • Annette Macleod, University of Glasgow, UK • Philippe Büscher, ITM Antwerp, Belgium • Bruno Bucheton, IRD Marseille, France • Neil Hall/Christiane Hertz-Fowler, University of Liverpool, UK • Mike Parker, University of Oxford, UK
Co-applicants
Collaborators
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RHDGen Network – Genetics of rheumatic heart disease Bongani Mayosi Department of Medicine University of Cape Town • Raj Ramesar, University of Cape Town, South Africa • Nicola Mulder, University of Cape Town, South Africa • Andrew Whitelaw, New Groote Schuur Hospital, South Africa • Stephen Ogendo, University of Nairobi, Kenya • Ana Mocumbi, Instituto Nacional de Saude, Mozambique • Christopher Hugo-Hamman, CBMH, South Africa • Okechukwu Ogah, University College Hospital, Nigeria • Ahmed El Sayed, Khartoum, Sudan • Charles Mondo, Uganda Heart Institute, Uganda • John Musuku, University of Zambia, Zambia • Guillaume Pare, McMasters University, Canada • Bernard Keavney/Heather Cordell, Newcastle University, UK • James Dale, University of Tennessee, USA • Mike Parker, University of Oxford, UK
Co-applicants
Collaborators
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Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa Albert Amoah University of Ghana, Ghana
• Clement Adebamowo, Institute of Human Virology, Nigeria • Pontiano Kaleebu, Uganda Virus Research Institute, Uganda • Saidi Kapiga, NIMR, Tanzania • Naomi Levitt, University of Cape Town, South Africa • Ayesha Ahmed Motala, UKZN, South Africa • Moffat Nyirenda, University of Malawi, Malawi • Charles Rotimi, NHGRI, USA • Manjinder Sandhu, Wellcome Trust Sanger Institute, UK • Eugene Sobngwi, University of Yaoundé, Cameroon • Mark McCarthy/Mike Parker, University of Oxford, UK • Dominic Kwiatkowski, Wellcome Trust Sanger Institute, UK • Branwen Hennig/Liam Smeeth, LSHTM, UK • Naby Moussa Balde, SED, Guinée • Sophie Hawkesworth, MRC Gambia, The Gambia • Patricia Marshall, Case Western Reserve, USA
Co-applicants
Collaborators
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H3Africa as a Consortium….
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Consortium approach
• Individual projects funded under H3Africa would come under the H3Africa ‘umbrella’
• Funders envisioned a Consortium approach, such
HapMap, WTCCC and the 1000 Genomes Project
• Maximise the benefit and impact of the H3Africa Consortium
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Could be thought of as a ‘Participatory Democracy’ ‘Aims to create opportunities for all members of a Consortium [population] to make meaningful contributions to decision-making and to obtain as broad a range of views as possible’
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Steering Commi,ee
Data Access Commi,ee
To be established
Independent Expert
Commi,ee
Lead Inves=gators NIH staff WT staff
?
Biorepository Users
Publica=on & Marker paper
Data Sharing, Access & Release
Ethics & Regulatory Issues
Phenotype Harmonisa=on
Genotype Analysis
Comms & Public Outreach
Educa=on & Training
Study Coordinators
Biorepository Commi,ee
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Challenges • Participants need to buy-in to the structure and
overarching goals
• Can be burdensome for participants, eg Working Groups, Steering Committee calls
• Individual preferences or ways of working may need to adapt and change
• Consortia need to flexible and change over time
• Communication essential – internally and externally
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Benefits • Shared resources
• Exchange of ideas
• Centralised resources, eg H3ABioNet
• Standardized operating procedures, methods and analysis schemes
• Access to training, bioinformatics and analysis pipelines
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Benefits cont’d…. • Added value from cross-project and cross-consortium
collaborations
• Shared risk
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What do we need from you?
• Participation!
• Working Groups • Steering Committee
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Consortium Coordinating Centre
• Provide support for trans-H3Africa Consortium activities
• • Will employ an administrator and coordinator • • Will provide support for the Working Groups and
H3Africa Steering Committee • • Reports to the Steering Committee
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Samples deposition • Deposition of biological samples into NIH-funded
biorepositories is not a condition of WT award • Concern there would be challenges in using
biorepositories, such as moving samples across borders,
• It is the expectation that Trust-funded samples will be
deposited, if no barriers exist
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Questions?
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“TrypanoGEN – genetic determinants of susceptibility to trypanosomiasis”
Enock Matovu College of Veterinary Medicine Makerere University, Uganda
• Vision: • Develop an integrated study of human, parasite and vector genetic variation in trypanosomiasis
• Initial high level objectives: • Create a biobank of retrospective and prospective samples • Generate a database of human genetic variation across Africa
Re-sequencing of
African population N=160 from 4 centres to estimate unobserved SNPs
Discovery cohort 600 stage 1 and 2 patients 200 asymptomatic controls 500 population controls
Validation cohort of 1% top hits
400 Stage 1 and 2 patients 200 asymptomatic controls 900 population controls
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“TrypanoGEN – genetic determinants of susceptibility to trypanosomiasis”
• Issa Sidibe, CIRDES, Burkina Faso • Dieudonne Mumba, INRB, Democratic Republic of Congo • Mathurin Koffi, University of Abob-Adjame, Côte d’Ivoire • Gustave Simo, University of Dschang, Cameroon • John Enyaru, Makerere University, Uganda • Martin Simuunza, University of Zambia, Zambia • John Chisi, University of Malawi, Malawi • Stafford Kibona, NIMR, Tanzania • Vincent Pius Alibu, Makerere University, Uganda • Annette Macleod, Glasgow, UK • Philippe Büscher, ITM Antwerp, Belgium • Bruno Bucheton, IRD Marseille, France • Neil Hall/Christiane Hertz-Fowler, Liverpool, UK • Mike Parker, Oxford, UK
Co-applicants
Collaborators
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“RHDGen Network – Genetics of rheumatic heart disease”
Bongani Mayosi Department of Medicine University of Cape Town
• High level aim: • Broaden understanding of RHD pathogenesis in sub-Saharan Africa
by identifying resistance and susceptibility genes
Case-control study 1500 cases 1500 controls …to discover SNPs associated with RHD
Family-based GWAS 1000 independent cases 2000 parents …to confirm or refute significant hits
Combined analysis 2500 cases 2500 controls/pseudo-controls …to identify associations of smaller effect size
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The H3Africa Initiative
“RHDGen Network – Genetics of rheumatic heart disease”
• Raj Ramesar, University of Cape Town, South Africa • Nicola Mulder, University of Cape Town, South Africa • Andrew Whitelaw, New Groote Schuur Hospital, South Africa • Stephen Ogendo, University of Nairobi, Kenya • Ana Mocumbi, Instituto Nacional de Saude, Mozambique • Christopher Hugo-Hamman, CBMH, South Africa • Okechukwu Ogah, University College Hospital, Nigeria • Ahmed El Sayed, Khartoum, Sudan • Charles Mondo, Uganda Heart Institute, Uganda • John Musuku, University of Zambia, Zambia • Guillaume Pare, McMasters University, Canada • Bernard Keavney/Heather Cordell, Newcastle University, UK • James Dale, University of Tennessee, USA • Mike Parker, University of Oxford, UK
Co-applicants
Collaborators
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“Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa”
Albert Amoah University of Ghana, Ghana
• High level aim: • Assess burden and aetiology of type 2 diabetes and its complications in adult populations across sub-Saharan Africa
• Initial development of epidemiological and genomic resource: • Recruitment of up to 1000 cases from each of 12 centres (diabetes clinics, hospitals, referral centres, tertiary clinics) • Population-based cross-sectional survey
• Possible genomics projects: • Re-sequencing of candidate regions at high coverage of 4000 participants • Sequencing of 500-600 genomes at low coverage • Whole genome sequencing of 1000 participants • Genotyping of 1500 participants
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“Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa”
• Clement Adebamowo, Institute of Human Virology, Nigeria • Pontiano Kaleebu, UVRI, Uganda • Saidi Kapiga, NIMR, Tanzania • Naomi Levitt, University of Cape Town, South Africa • Ayesha Ahmed Motala, UKZN, South Africa • Moffat Nyirenda, University of Malawi, Malawi • Charles Rotimi, NHGRI, USA • Manjinder Sandhu, Wellcome Trust Sanger Institute, UK • Eugene Sobngwi, University of Yaoundé, Cameroon • Mark McCarthy/Mike Parker, University of Oxford, UK • Dominic Kwiatkowski, Sanger Institute, UK • Branwen Hennig/Liam Smeeth, LSHTM, UK • Naby Moussa Balde, SED, Guinée • Sophie Hawkesworth, MRC Gambia, The Gambia • Patricia Marshall, Case Western Reserve, USA
Co-applicants
Collaborators
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Disease burden in Africa
Poverty +
Limited access to affordable modern health care =
Disproportionate burden of disease
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Differences in disease prevalence* Environmental factors
+ Human genomic factors
= Vast differences in disease prevalence between
• Countries
• Geographic regions within a country
• Ethnic groups in the same geographic region
* all individuals affected by a disease within a particular period of time
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Contemporary genetic and genomics research in Africa? • African populations and their genetic variation in the
context of disease are understudied
• African researchers are underrepresented in modern genetics and genomics research
• African research capacity to undertake population-based genetics and genomics research is underdeveloped
Human Heredity and Health in Africa = H3Africa
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The vision of H3Africa
“To facilitate an African-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”
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NIH and Wellcome Trust join forces • Announcement of partnership between the NIH and
the Wellcome Trust (June 2010)
• White Paper “Harnessing genomic technologies toward improving health in Africa” (February 2011)
• H3Africa conference in Cape Town (March 2011)
£15m
£8m
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WT call for proposals
NIH calls for proposals
Awards
• Bioinformatics Network • Biorepository Grants • Collaborative Centres of Excellence
One initiative, multiple calls…
Joint announcement
• Themed Strategic Awards to support research networks
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Building on existing capacity • Cohort studies and demographic surveillance systems
• Networks
• MalariaGEN
• African Bioinformatics Network
• INDEPTH
• Training
• African Regional Training Centre for Bioinformatics
and Applied Genomics
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Building on NIH and WT investments
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An introduction to the H3Africa Initiative
THANK YOU.
http://h3africa.org