Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA)
Lead Research Organisation:
University of Cambridge
Abstract
The research proposal brings together a series of independent research programmes to study non-communicable diseases (NCDs), including the impact of chronic infection-HIV and hepatitis viruses-on these diseases, across sub-Saharan Africa. With opportunities for research capacity strengthening and training, the partnership provides a unique research framework to design and conduct large scale studies that will provide more reliable and precise information on disease burden and underlying causes of these diseases. The partnership also provides a platform to increase critical mass and help foster research leadership at the institutions within the partnership. Importantly, the proposal brings together institutes with established and nascent research programmes aimed at studying NCDs at the population-level. The overall aim is to develop a sustainable partnership that will facilitate multi-centre research to assess the burden and aetiology of NCDs in SSA to improve the evidence base underpinning potential responses to NCDs, provide a platform for interventional research in NCDs, and to ensure that African populations benefit from the ongoing advances in genomics.
Technical Summary
The overall aim is to develop a sustainable partnership that will facilitate multi-centre research to assess the burden and aetiology of NCDs in SSA to improve the evidence base underpinning potential responses to NCDs, provide a platform for interventional research in NCDs, and to ensure that African populations benefit from the ongoing advances in genomics.
Specific objectives are to 1) establish a consortium of investigators and research institutes capable of conducting multi-centre research into NCDs in SSA; 2) devise and develop guidelines for research governance and scientific strategy for the NCD partnership; 3) devise and maintain a web-portal for sharing data, research resources (data collection tools and software, e-questionnaires, protocols, SOPs, analytical plans), and research training tools with the wider scientific community; 4) facilitate capacity strengthening, provide research training, and identify mechanisms to develop infrastructure for NCD population based research (observational studies, including genomic analyses, and intervention trials) in SSA; 5) enhance ongoing studies across the partnership by facilitating pooled collaborative analyses across multiple regions of SSA; and 6) develop partnership-wide research funding proposals.
Specific objectives are to 1) establish a consortium of investigators and research institutes capable of conducting multi-centre research into NCDs in SSA; 2) devise and develop guidelines for research governance and scientific strategy for the NCD partnership; 3) devise and maintain a web-portal for sharing data, research resources (data collection tools and software, e-questionnaires, protocols, SOPs, analytical plans), and research training tools with the wider scientific community; 4) facilitate capacity strengthening, provide research training, and identify mechanisms to develop infrastructure for NCD population based research (observational studies, including genomic analyses, and intervention trials) in SSA; 5) enhance ongoing studies across the partnership by facilitating pooled collaborative analyses across multiple regions of SSA; and 6) develop partnership-wide research funding proposals.
Planned Impact
The partnership will provide a platform for research that will allow a robust and accurate assessment of the burden of non-communicable diseases (NCDs) and help identify risk factors for infectious diseases and NCDs among populations in sub-Saharan Africa, informing governments and health agencies (local and international). This will primarily be communicated through scientific reports and healthy policy recommendations. This in turn may help inform health service planning and shape preventative and therapeutic strategies for NCDs across the region. Although individual centres vary, there is also some direct benefit to participants in the individual studies conducted at respective collaborating centres in relation to feedback and support for health indices, such as high blood pressure or obesity; however, the current proposal seeks to harmonise and utilise existing data and resources to assess the burden and causes of NCDs in sub-Saharan Africa.
For countries in SSA to benefit from future progress in NCD epidemiology, public health and genomics, there is a need to strengthen research capacity, training and collaboration across the region to ensure researchers can play a full part. The partnership will be underpinned by capacity-strengthening activities, including facilitating and promoting NCD epidemiological and genomic research, mechanisms and infrastructure to share research resources (study protocols, SOPs, e-questionnaires, data access), and training and support for the next generation of research leaders in Africa. As a concrete example, we propose to establish a one week course in the epidemiology and public health aspects of "global chronic disease epidemiology" with particular emphasis on regions undergoing epidemiological transition and the interrelation among chronic infection and NCDs. The development of this course will be led by the University of Witwatersrand and it will be a direct development of an existing course in chronic disease epidemiology embedded within the masters training programmes in epidemiology and public health at the University. To facilitate studies within the partnership, and to provide sustainable capacity building, we plan to develop a bioinformatics hub at the MRC/UVRI Uganda centre to facilitate data storage, management and access across centres. We aim to enhance existing capacity through the expansion of the existing network and server system and with the addition of a full-time data manager.
The NCD research community - particularly researchers working in African centres - will benefit from this investment in training and infrastructure; thus the partnership will provide an excellent framework to develop a sustainable international research programme for NCDs in SSA.
With the development of an international research partnership, including sharing joint resources, samples and data, and to ensure its sustainability (by developing local scientific leadership) and equable access to resources, it will be important to put in place mechanisms for research and resource governance. We aim to formalise such a mechanism within the partnership. Equally, this governance structure will provide a mechanism for the wider scientific community to access data and resources generated through the partnership, including electronic tools for data collection, harmonisation and analyses. More specifically, in the context of secondary research, efforts to harmonise study methods and data across centres, including the development of consensus documents, methods and tools that optimise the ability of contributing centres and researchers to participate and collaborate in cutting-edge science, will be a major focus of this partnership. These efforts will span key research disciplines including ethico-legal approaches, epidemiology, sample handling, genomics, information management systems, and biostatistics.
Commercial exploitation is not anticipated.
For countries in SSA to benefit from future progress in NCD epidemiology, public health and genomics, there is a need to strengthen research capacity, training and collaboration across the region to ensure researchers can play a full part. The partnership will be underpinned by capacity-strengthening activities, including facilitating and promoting NCD epidemiological and genomic research, mechanisms and infrastructure to share research resources (study protocols, SOPs, e-questionnaires, data access), and training and support for the next generation of research leaders in Africa. As a concrete example, we propose to establish a one week course in the epidemiology and public health aspects of "global chronic disease epidemiology" with particular emphasis on regions undergoing epidemiological transition and the interrelation among chronic infection and NCDs. The development of this course will be led by the University of Witwatersrand and it will be a direct development of an existing course in chronic disease epidemiology embedded within the masters training programmes in epidemiology and public health at the University. To facilitate studies within the partnership, and to provide sustainable capacity building, we plan to develop a bioinformatics hub at the MRC/UVRI Uganda centre to facilitate data storage, management and access across centres. We aim to enhance existing capacity through the expansion of the existing network and server system and with the addition of a full-time data manager.
The NCD research community - particularly researchers working in African centres - will benefit from this investment in training and infrastructure; thus the partnership will provide an excellent framework to develop a sustainable international research programme for NCDs in SSA.
With the development of an international research partnership, including sharing joint resources, samples and data, and to ensure its sustainability (by developing local scientific leadership) and equable access to resources, it will be important to put in place mechanisms for research and resource governance. We aim to formalise such a mechanism within the partnership. Equally, this governance structure will provide a mechanism for the wider scientific community to access data and resources generated through the partnership, including electronic tools for data collection, harmonisation and analyses. More specifically, in the context of secondary research, efforts to harmonise study methods and data across centres, including the development of consensus documents, methods and tools that optimise the ability of contributing centres and researchers to participate and collaborate in cutting-edge science, will be a major focus of this partnership. These efforts will span key research disciplines including ethico-legal approaches, epidemiology, sample handling, genomics, information management systems, and biostatistics.
Commercial exploitation is not anticipated.
Organisations
- University of Cambridge (Collaboration, Lead Research Organisation)
- University of Conakry (Collaboration)
- University of KwaZulu-Natal (Collaboration)
- MENTOR Initiative (Collaboration)
- Haydom Lutheran Hospital (Collaboration)
- Cohort of RIS (CoRIS) (Collaboration)
- Moi University (Collaboration)
- National Institute for Medical Research, Tanzania (Collaboration)
- University College Hospital (Collaboration)
- Homerton University Hospital NHS Foundation Trust (Collaboration)
- MRC/UVRI Uganda Research Unit on AIDS (Collaboration)
- CAMBRIDGE UNIVERSITY HOSPITALS NHS FOUNDATION TRUST (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- PHAEDRA, Sydney AIDS Prospective Study and Sydney Primary HIV Infection Cohort (Collaboration)
- Southern Alberta Clinic (SAC) (Collaboration)
- Pasteur Institute, Algiers (Collaboration)
- Pontifical Catholic University of Ecuador (Collaboration)
- Newcastle University (Collaboration)
- University of Nigeria (Collaboration)
- Institute of Human Virology (Collaboration)
- West Hertfordshire Hospitals NHS Trust (Collaboration)
- University of Maryland, College Park (Collaboration)
- Armed Forces Research Institute of Medical Sciences (Collaboration)
- Tribhuvan University of Nepal (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- Royal Cornwall Hospitals NHS Trust (Collaboration)
- London School of Hygiene and Tropical Medicine (LSHTM) (Collaboration)
- National Institutes of Health (NIH) (Collaboration)
- St Thomas' Hospital (Collaboration)
- Central and North West London NHS Foundation Trust (Collaboration)
- University of the Gambia (Collaboration)
- Corporate Policy Unit (Collaboration)
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) (Collaboration)
- Academy of Medical Sciences (AMS) (Collaboration)
- Kenyan Institute for Medical Research (KEMRI) (Collaboration)
- Italian Cohort of Antiretroviral Naïve Patients (ICONA) (Collaboration)
- H3Africa (Collaboration)
- Lyon Primary Infection Cohort (LPIC) (Collaboration)
- Makerere University (Collaboration)
- University of Lausanne (Collaboration)
- National Human Genome Center; Howard University (Collaboration)
- VU University Medical Center (Collaboration)
- Institute of Development Research (IRD) (Collaboration)
- St George's Healthcare NHS Trust (Collaboration)
- University of Virginia (UVa) (Collaboration)
- Austrian HIV Cohort Study (AHIVCOS) (Collaboration)
- University of Sussex (Collaboration)
- UNIVERSITY OF GHANA (Collaboration)
- University of Malawi (Collaboration)
- Uganda Christian University (Collaboration)
- Sheffield Teaching Hospitals NHS Foundation Trust (Collaboration)
- German HIV-1 Seroconverter Cohort (Collaboration)
- National and Kapodistrian University of Athens (Collaboration)
- Stony Brook University (Collaboration)
- Henry Stewart Conferences and Events (Collaboration)
- Charing Cross Hospital (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- University of Bamako (Collaboration)
- University of Buea (Collaboration)
- Amsterdam Medical Center (Collaboration)
- University of Geneva (Collaboration)
- Ethiopian Public Health Institute (Collaboration)
- University of Ibadan (Collaboration)
- Primary Infection Cohort (PRIMO) (Collaboration)
- InfCare Swedish Cohort (Collaboration)
- Wellcome Trust (Collaboration)
- Amsterdam Cohort Study Among Homosexual Men (Collaboration)
- St Mary's Hospital, London (Collaboration)
- Loyola University Medical Center (Collaboration)
- International AIDS Vaccine Initiative (IAVI) (Collaboration)
- University of Yaoundé (Collaboration)
- UK Register of HIV Seroconverters (UKRHS) (Collaboration)
- Makerere University College of Health Sciences (Collaboration)
- Chelsea and Westminster Hospital NHS Foundation Trust (Collaboration)
- Walter Reed Afrims Research Unit (Collaboration)
- Aix-Marseille University (Collaboration)
- European Organization for Nuclear Research (CERN) (Collaboration)
- African Society for Bioinformatics and Computational Biology (Collaboration)
- Malawi Epidemiology & Intervention Research Unit (Collaboration)
- Armauer Hansen Research Institute (Collaboration)
- Stellenbosch University (Collaboration)
- University of Oxford (Collaboration, Project Partner)
- University of the Witwatersrand (Collaboration)
- Foundation for the National Institutes of Health (FNIH) (Collaboration)
- St-Pierre, Belgium (COHERE) (Collaboration)
- University of Cape Town (Collaboration)
- Lebanese American University (Collaboration)
- University College London (Collaboration)
- BARTS HEALTH NHS TRUST (Collaboration)
- Addis Ababa University (Collaboration)
- National Centre for Research and Training on Malaria (Collaboration)
- PORTSMOUTH HOSPITALS NHS TRUST (Collaboration)
- International Centre for Research and Development of Livestock in Subhumid (CIRDES) (Collaboration)
- St Richard's Hospital (Collaboration)
- East and North Hertfordshire NHS Trust (Collaboration)
- King's College London (Collaboration)
- University of Liverpool (Collaboration)
- London School of Hygiene & Tropical Medicine (Project Partner)
Publications
Allcock S
(2017)
Antimicrobial resistance in human populations: challenges and opportunities.
in Global health, epidemiology and genomics
Allcock SH
(2019)
Sociodemographic patterns of health insurance coverage in Namibia.
in International journal for equity in health
Allcock SH
(2018)
A cross-sectional analysis of ITN and IRS coverage in Namibia in 2013.
in Malaria journal
Asiki G
(2013)
The general population cohort in rural south-western Uganda: a platform for communicable and non-communicable disease studies.
in International journal of epidemiology
Barr AL
(2018)
Objective measurement of physical activity: improving the evidence base to address non-communicable diseases in Africa.
in BMJ global health
Barr AL
(2016)
The need for an integrated approach for chronic disease research and care in Africa.
in Global health, epidemiology and genomics
Chen J
(2019)
Genome-wide association study of type 2 diabetes in Africa
in Diabetologia
| Description | IAVI/UMIC collaboration agreement |
| Amount | £623,682 (GBP) |
| Organisation | United States Agency for International Development |
| Sector | Public |
| Country | United States |
| Start | 06/2016 |
| End | 07/2021 |
| Description | Medical bioinformatics strategic award |
| Amount | £2,830,000 (GBP) |
| Funding ID | MR/L016273/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2014 |
| End | 12/2018 |
| Description | Network of Excellence |
| Amount | £180,000 (GBP) |
| Funding ID | 260694 |
| Organisation | European Commission |
| Department | Seventh Framework Programme (FP7) |
| Sector | Public |
| Country | European Union (EU) |
| Start | 11/2012 |
| End | 11/2015 |
| Title | Ugandan Medical Informatics Centre (UMIC) |
| Description | The Ugandan Medical Informatics Centre (UMIC) provides a high end computational resource for studies all over Africa which will require big data analysis and storage. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | - Provision of trainings on medical informatic techniques for African students. - Integration and curation of large data sets originated from population studies within the continent. - Computational resources available to APCDR partners to conduct genomic and population studies. - Building the capacity of Ugandan Bioinformaticians through collaborative skills sharing and training, enabling local Bioinformaticians to take leading roles in the operations of the data centre. |
| Title | AGR - ADRP and Transcriptomics |
| Description | The overarching theme of the African Genomic Resources (AGR) project is to design and create resources to support medical genetic studies in Africa. Within this framework we have developed: 1) a continent-specific whole genome sequence reference panel for imputation and array design, 2) a continent-specific transcriptome panel for the interpretation of genome wide association data. Whole genome sequencing projects such as HapMap, 1000 Genomes, UK10K and Genomes of the Netherlands have allowed the generation of large and diverse haplotype reference panels for humans. In spite of these efforts, sequences available from populations within Africa have been limited, and are not representative of the genetic diversity across the continent. Recent efforts such as the African Genome Variation Project (AGVP), Ethiopian diversity panels and UG2G (Uganda 2000) have greatly expanded on these resources, producing the largest panels of sequence data from Africa to date. The African Diversity Reference Panel (ADRP) integrates all of these resources with additional sequences from diverse populations across Africa, with the aim of providing a continent-specific reference panel as a resource for medical genetics in Africa and globally. This panel will provide the largest resource of diverse haplotypes across Africa to date, contributing to initiatives such as the Haplotype Consortium, accessible to researchers worldwide. As part of the African Genome Resource (AGR) project we aim to create an African transcriptome panel. Using 1000Genomes cell lines, we generated high coverage RNAseq data (Illumina HiSeq) from 6 different populations across Africa; the first large-scale resource to examine eQTLs within Africa. Specifically we sequenced transcriptomes from 600 unrelated individuals from six populations from West (Gambian, The Gambia; Mende, Sierra Leone; Esan and Yoruba, Nigeria) and East Africa (Luhya and Masai, Kenya). Such a resource will help understand the transcriptional landscape in African populations, population differences in the diversity of splicing isoforms, as well as identify novel transcripts and exons across the genome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | We envisage that this panel of diverse populations across Africa will increase imputation accuracy across the allele frequency spectrum, and improve the statistical power for any SNP array based GWAS carried out in Africa. This panel will additionally inform efforts to design efficient continent specific SNP arrays, with better coverage across African populations. The African transcriptome panel is the first large-scale resource to examine eQTLs within Africa.Such a resource will help understand the transcriptional landscape in African populations, population differences in the diversity of splicing isoforms, as well as identify novel transcripts and exons across the genome. It will be invaluable for the interpretation of findings from large-scale GWAS being conducted in Africa, supporting initiatives such as the H3A consortium. |
| URL | https://imputation.sanger.ac.uk/?about=1 |
| Title | African Genome Variation (AGV) |
| Description | The AGV data includes dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | The African Genome Variation (AGV) data provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. Given the marked genetic diversity across populations across SSA, the use of reference imputation panels from SSA populations for other SSA populations, may improve imputation accuracy compared with other population groups we therefore used sequence data to generate an African reference panel for imputation. This will serve as a resource in addition to existing panels. |
| URL | https://www.ebi.ac.uk/ega/home |
| Title | UG2G |
| Description | whole genome sequence data on up to 1,978 individuals spanning 41.5M SNPs and 4.5M indels |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | We highlight the value of the largest sequence panel from Africa to date as a global resource for variant discovery, imputation and understanding the mutational spectrum and its clinical relevance in African populations. |
| URL | https://www.ebi.ac.uk/ega/studies/EGAS00001000545 |
| Title | UGWAS |
| Description | data from 4,778 individuals with genotypes for ~2.2 million SNPs from the Uganda GWAS resource (UGWAS) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Genomic studies in African populations provide unique opportunities to understand disease aetiology, human genetic diversity and population history in a regional and a global context. |
| URL | https://www.ebi.ac.uk/ega/studies/EGAS00001001558 |
| Description | 100k Genomes in Africa Study |
| Organisation | Amsterdam Medical Center |
| Country | Netherlands |
| Sector | Hospitals |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | Ethiopian Public Health Institute |
| Country | Ethiopia |
| Sector | Public |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | International AIDS Vaccine Initiative (IAVI) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | Kenyan Institute for Medical Research (KEMRI) |
| Country | Kenya |
| Sector | Public |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | MRC/UVRI Uganda Research Unit on AIDS |
| Country | Uganda |
| Sector | Public |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | Malawi Epidemiology & Intervention Research Unit |
| Country | United Kingdom |
| Sector | Learned Society |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | University of KwaZulu-Natal |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | 100k Genomes in Africa Study |
| Organisation | University of Yaoundé |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | With varying environments and adaptation, the spectrum and distribution of risk factors for a broad range of cardiometabolic and infectious disease and their individual contribution may differ in African populations compared with European populations or those of African descent in Europe, North America or elsewhere. The planned work will allow us to address the following question: Can we better understand the genetic determinants of cardiometabolic traits and diseases through genomic studies in African populations, including their population specificity in a global context? WTSI and UCAM will collaborate to receive and process pseudonymised biological samples and generate and analyse genomic data, in association with relevant phenotypic data. WTSI and UCAM support for this may include DNA extraction, sample shipment, and genotyping and sequencing |
| Collaborator Contribution | Partners will provide blood or DNA samples and phenotyped data from their study collections. They will also contribute to data analyses. |
| Impact | no output yet. |
| Start Year | 2016 |
| Description | African Genome Variation (AGV) |
| Organisation | Addis Ababa University |
| Country | Ethiopia |
| Sector | Academic/University |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | MRC/UVRI Uganda Research Unit on AIDS |
| Country | Uganda |
| Sector | Public |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | National Institutes of Health (NIH) |
| Department | Centre for Research on Genomics and Global Health (CRGGH) |
| Country | United States |
| Sector | Public |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | University of KwaZulu-Natal |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Genome Variation (AGV) |
| Organisation | University of the Witwatersrand |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | This work aims to facilitate large-scale genetic association studies in diseases of relevance to SSA populations by providing first insights into the genetic variation landscape of different ethnic groups across SSA. My research team genotyped 100 unrelated individuals from each of several ethnic or ethno-linguistic groups on the 2.5 million SNP Illumina HumanOmni chip. To corroborate our analyses we also included whole genome sequences for three of these groups. This work will inform genomic epidemiological studies in SSA by providing a reference for allelic, haplotype and linkage disequilibrium (LD) structure for common variants in populations not covered by the HapMap project. This project has been designed to provide a currently unavailable genome-wide view of common variation and a framework for statistically imputing genetic variants for genome wide association studies in anticipation of future larger-scale whole-genome sequencing endeavours in relevant populations. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa provided existing (biobanked) sample collections with appropriate research ethics consent. Most of these partners were also directly involved in the analyses of the resulting data. |
| Impact | The overarching aim of this project was to characterise common (minor allele frequency > 5 percent) sequence variation in SSA populations in order to facilitate the design of powerful genetic association studies. Specifically, we will aim to: 1) examine the allele frequency spectrum of variants on the chip; 2) characterise patterns of LD and haplotype structure; 3) evaluate optimal study designs for African genomics; 4) investigate imputation-based approaches aiming to increase genetic association study power; 5) identify analytical challenges and develop statistical genetics methods to address them; 6) generate a valuable resource for the scientific community; 7) promote collaboration and synergies among contributing parties; and 8) provide a research framework and resource for additional analyses, for example studies of genome-wide selection, mapping genetic variation to linguistic and demographic differences, and evaluating powerful approaches for trans-ethnic meta-analysis and fine-mapping. The first manuscript has been accepted for publication: Deepti Gurdasani , †, Tommy Carstensen1,2†, Fasil Tekola-Ayele †, Luca Pagani1†, Ioanna Tachmazidou1†, Konstantinos Hatzikotoulas1, Savita Karthikeyan1,2, Louise Iles1,2, Martin O. Pollard1, Ananyo Choudhury , Graham R. S. Ritchie1, , Yali Xue1, Jennifer Asimit1, Rebecca N. Nsubuga , Elizabeth H. Young1,2, Cristina Pomilla1,2, Katja Kivinen1, Kirk Rockett , Anatoli Kamali6, Ayo P. Doumatey3, Gershim Asiki6, Janet Seeley6, Fatoumatta Sisay-Joof , Muminatou Jallow8, Stephen Tollman4, , Ephrem Mekonnen , Rosemary Ekong , Tamiru Oljira10, Neil Bradman , Kalifa Bojang8, Michele Ramsay4, Adebowale Adeyemo3, Endashaw Bekele10, Ayesha Motala , Shane A. Norris4, Fraser Pirie13, Pontiano Kaleebu6, Dominic Kwiatkowski1, Chris Tyler-Smith1‡, Charles Rotimi3‡, Eleftheria Zeggini1‡ and Manjinder S. Sandhu1,2‡. (In press) The African Genome Variation Project shapes medical genetics in Africa. Nature |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Institute of Human Virology |
| Country | Nigeria |
| Sector | Charity/Non Profit |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Makerere University College of Health Sciences |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Centre for Genomics and Global Health |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Unit, The Gambia |
| Country | Gambia |
| Sector | Public |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Medical Research Council (MRC) |
| Department | MRC/UVRI and LSHTM Research Unit Uganda |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Moi University |
| Department | School of Medicine |
| Country | Kenya |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | National Human Genome Center; Howard University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | National Institute for Medical Research, Tanzania |
| Department | Mwanza Intervention Trials Unit (MITU) |
| Country | Tanzania, United Republic of |
| Sector | Public |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | National Institutes of Health (NIH) |
| Department | National Human Genome Research Institute (NHGRI) |
| Country | United States |
| Sector | Public |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Cambridge |
| Department | MRC Epidemiology Unit |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Cape Town |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Conakry |
| Country | Guinea |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Ghana |
| Department | School of Medicine |
| Country | Ghana |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Ibadan |
| Country | Nigeria |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of KwaZulu-Natal |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Nigeria |
| Department | University of Nigeria Teaching Hospital (UNTH) Ituku/Ozalla Enugu |
| Country | Nigeria |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Oxford |
| Department | Wellcome Trust Centre for Human Genetics |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of Yaoundé |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of the Gambia |
| Country | Gambia |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | University of the Witwatersrand |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Partnership for Chronic Disease Research |
| Organisation | Wellcome Trust |
| Department | Malawi-Liverpool Wellcome Trust Clinical Research Programme |
| Country | Malawi |
| Sector | Academic/University |
| PI Contribution | 1. Set-up and coordination of the partnership. 2. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 3. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 18 centres from 12 different countries. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, bioethics, population-based surveys and interventions. African centres also contribute existing resources and infostructure for sample collection (clinics and field stations) and analyses. |
| Impact | Two successful grant application have resulted so far from this partnership: Wellcome Trust (WT099316MA) Burden, spectrum and aetiology of type 2 diabetes in sub-Saharan Africa 2013-2018 £2,550,000 MRC Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA) 2013-2018 £885,314 The partnership is also taking part in several ongoing projects including the African Genome Variation project, led by the Wellcome Trust sanger Institute, and a HIV/ART/NCD meta-analysis. |
| Start Year | 2011 |
| Description | African Society for Bioinformatics and Computational Biology (ASBCB) |
| Organisation | African Society for Bioinformatics and Computational Biology |
| Country | Tunisia |
| Sector | Learned Society |
| PI Contribution | Award of 13 Travel Fellowships for students to attend African Society for Bioinformatics and Computational Biology (ASBCB) Conference in Entebbe, Uganda October 10-13 2017 |
| Collaborator Contribution | Enable the students to attend workshops in Bioinformatics, and provide an avenue for students to present their work. All 13 students, presented their work either by oral presentation of in poster format. |
| Impact | Facilitation of training in Bioinformatics and computational biology in Africa |
| Start Year | 2017 |
| Description | EuroCoord Network of Excellence |
| Organisation | Amsterdam Cohort Study Among Homosexual Men |
| Country | Netherlands |
| Sector | Charity/Non Profit |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Austrian HIV Cohort Study (AHIVCOS) |
| Country | Austria |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Cohort of RIS (CoRIS) |
| Country | Spain |
| Sector | Hospitals |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | German HIV-1 Seroconverter Cohort |
| Country | Germany |
| Sector | Charity/Non Profit |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | InfCare Swedish Cohort |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | International AIDS Vaccine Initiative (IAVI) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Italian Cohort of Antiretroviral Naïve Patients (ICONA) |
| Country | Italy |
| Sector | Charity/Non Profit |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Lyon Primary Infection Cohort (LPIC) |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | National and Kapodistrian University of Athens |
| Department | Athens Multicentre AIDS Cohort Study (AMACS) |
| Country | Greece |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | PHAEDRA, Sydney AIDS Prospective Study and Sydney Primary HIV Infection Cohort |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Primary Infection Cohort (PRIMO) |
| Country | France |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | Southern Alberta Clinic (SAC) |
| Country | Canada |
| Sector | Hospitals |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | St-Pierre, Belgium (COHERE) |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | EuroCoord Network of Excellence |
| Organisation | UK Register of HIV Seroconverters (UKRHS) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | EuroCoord (funded by EC FP7) is a Network of Excellence established by several of the biggest HIV cohorts and collaborations within Europe - CASCADE, COHERE, EuroSIDA, and PENTA. My team is leading the project 'Genomic Studies of HIV Control in the CASCADE Collaboration', which is part of one of EuroCoord workpackages. The aim of this project is to examine the genetic differences contributing to viral and disease control in HIV infection, by identifying rare host and virus genetic variants in individuals at the two extremes of the immunological and clinical spectrum. Specifically we will sequence exomes from 200 individuals: roughly 100 individuals belonging to the 'elite-LTNP' group and 100 individuals from the 'rapid progression' group. |
| Collaborator Contribution | EuroCoord partners are grouped into: - Founding networks - Beneficiaries - Third parties We are part of the 'beneficiaries'. Listed above are the cohort studies, part of the 'founding networks', which are contributing to our project. The project use existing data and existing samples (blood and DNA) previously collected as part of the HIV cohort studies. The patner cohort studies identified eligible participants from study records at the originating study sites and provided samples and data. |
| Impact | We have already collated most samples for the project and analyses are underway. |
| Start Year | 2012 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Addis Ababa University |
| Country | Ethiopia |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Aix-Marseille University |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Armauer Hansen Research Institute |
| Country | Ethiopia |
| Sector | Charity/Non Profit |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Corporate Policy Unit |
| Country | South Africa |
| Sector | Public |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Henry Stewart Conferences and Events |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Institute of Development Research (IRD) |
| Department | IRD Centre de Montpelier |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Institute of Development Research (IRD) |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | International Centre for Research and Development of Livestock in Subhumid (CIRDES) |
| Country | Burkina Faso |
| Sector | Charity/Non Profit |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Lebanese American University |
| Country | Lebanon |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Loyola University Medical Center |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | MENTOR Initiative |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | MRC/UVRI Uganda Research Unit on AIDS |
| Country | Uganda |
| Sector | Public |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Makerere University |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | National Centre for Research and Training on Malaria |
| Country | Burkina Faso |
| Sector | Public |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | National Institutes of Health (NIH) |
| Department | Centre for Research on Genomics and Global Health (CRGGH) |
| Country | United States |
| Sector | Public |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Pasteur Institute, Algiers |
| Country | Algeria |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | Stony Brook University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University College London |
| Department | School of Life and Medical Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Bamako |
| Country | Mali |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Buea |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Cape Town |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Geneva |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Glasgow |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of KwaZulu-Natal |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Lausanne |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Liverpool |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Maryland |
| Department | Centre for Vaccine Development (CVD) |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Maryland |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Stellenbosch |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Stellenbosch |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Sussex |
| Department | Brighton and Sussex Medical School |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | University of Yaoundé |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Genetic Diversity in Africa Project (GDAP) |
| Organisation | VU University Medical Center |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Globally, human populations show structured genetic diversity as a result of geographical dispersion, selection and drift. Understanding this genetic variation can provide insights into our human origins and the evolutionary processes that shape both human adaptation and variation in disease.[1 2] In these contexts, Africa represents the ancestral birthplace of modern humans.[3] Populations from Africa have the highest levels of genetic diversity.[4 5] This characteristic, in addition to historical genetic admixture, can lead to complexities in the design of studies assessing the genetic determinants of disease and human variation. However, such studies of African populations are also likely to provide new opportunities to discover novel disease susceptibility loci and variants and refine gene-disease association signals.[3] A systematic assessment of genetic diversity within Africa would facilitate genomic epidemiological studies in the region. The Genome Diversity in Africa Project (GDAP) will importantly extend previous efforts to characterise population genetic diversity in Africa-informing population history and movement, evolutionary adaptation and disease susceptibility across Africa. Importantly, the GDAP will also help develop local resources and research capacity for public health and genomic epidemiological research, including approaches to strengthen research capacity, training, and collaboration across the region. Using a sequencing-based approach, GDAP aims to significantly advance the comprehensive catalogue of human genetic variation in Africa started by the African Genome Variation (AGV) project (African Genome Variation), including single nucleotide polymorphisms (SNPs), structural variants, and haplotypes. My research team will sequence at low and high depth the whole genome of around 100 individuals from each ethnolinguistic group, and complement these data with 2.5M Illumina array data from distinct regions within Africa. In total, we will aim to sequence up to 2,000 genomes. This resource will extend our understanding of our human origins, population history, and patterns of genetic diversity within and among populations in Africa. Furthermore, it will provide a global resource to help design, implement and interpret genomic studies in Africa populations and studies comprising globally diverse populations, thus complementing existing genomic resources. |
| Collaborator Contribution | Research groups and institutions, other consortia, and health organisations working in the fields of population health, health service provision, and genomics in Africa will provide existing (biobanked) or new sample collections with appropriate research ethics consent. Some of these partners will be also directly involved in the analyses of the resulting data. |
| Impact | This is a recent collaboration and there is no tangible putput yet however our scientific objectives are to: 1) develop a resource that provides a comprehensive catalogue of genetic variation in populations from Africa accessible to the global scientific community; 2) characterise population genetic diversity, structure, gene flow and admixture across Africa; 3) develop a cost-efficient, next-generation genotype array for diverse populations across Africa; 4) facilitate whole genome-sequencing association studies of complex traits and diseases by developing a reference panel for imputation and resource for enhancing fine-mapping disease susceptibility loci. These scientific objectives will be supported by cross-cutting operational activities, including network and management of the consortium, research ethics, and research capacity building in statistical genetics and bioinformatics. |
| Start Year | 2013 |
| Description | Global Chronic Disease Short Course |
| Organisation | University of the Witwatersrand |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | The APCDR had oversight for the strategy and design of the short course in close communication with the Wits team. The APCDR delegated certain administrative responsibilities to the Wits team, and directly handled travel bookings and contact with participants before during and after the short course. |
| Collaborator Contribution | A sub-team of APCDR members based at Wits did a first-round of recommendation of applications, and these recommendations were sent to the capacity building sub-committee for their approval. All recommendations were approved without changes. Wits did all the admin (handled by Kerstin, Busi and Dikgapha) apart from the flights, which were booked and handled by the University of Cambridge's designated travel agent, KeyTravel. A subcontract was set up to allow us to transfer APCDR funding to Wits to cover the costs of the 2015 short course. Kerstin published a blog on the short course on the GHEG journal website. |
| Impact | In total, 29 applications were received (see Appendix 3) and the Wits team recommended 15 candidates based on qualifications, scientific merit and institutional support. All recommendations were accepted by the sub-committee. The Wits team opted for an extra participant in place of a guest lecturer given the limited timeframe for securing an international guest for the course. Applicants applied from 8 countries; selected participants were residents of Cameroon, Nigeria, South Africa and Uganda. Of the original 29 applicants 8 were female, 20 were male and 1 did not disclose their gender. The 15 participants included 3 females and 12 males. Dr Kerstin Klipstein-Grobusch also published a blog about the short course: http://gheg-journal.co.uk/2015/10/building-african-capacity-in-chronic-disease-epidemiology/ |
| Start Year | 2015 |
| Description | H3A Diabetes |
| Organisation | Institute of Human Virology |
| Country | Nigeria |
| Sector | Charity/Non Profit |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | MRC/UVRI Uganda Research Unit on AIDS |
| Country | Uganda |
| Sector | Public |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | National Institute for Medical Research, Tanzania |
| Department | Mwanza Intervention Trials Unit (MITU) |
| Country | Tanzania, United Republic of |
| Sector | Public |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | National Institutes of Health (NIH) |
| Department | National Human Genome Research Institute (NHGRI) |
| Country | United States |
| Sector | Public |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | Newcastle University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | University of Cape Town |
| Department | Division of Endocrinology and Diabetic Medicine |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | University of Ghana |
| Department | School of Medicine |
| Country | Ghana |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | University of KwaZulu-Natal |
| Department | Department of Diabetes and Endocrinology |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | University of Malawi |
| Department | College of Medicine |
| Country | Malawi |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | University of Yaoundé |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3A Diabetes |
| Organisation | Wellcome Trust |
| Department | Malawi-Liverpool Wellcome Trust Clinical Research Programme |
| Country | Malawi |
| Sector | Academic/University |
| PI Contribution | 1. Expertise and research capacity in: genetics/genomics of chronic disease, informatics, large-scale analytical pipelines, statistical genetics, epidemiology and public health. 2. Access to high throughput next-generation sequencing and genotyping laboratory and analytical pipelines and infrastructure. |
| Collaborator Contribution | The partnership includes 10 centres directly and 16 centres in total. Expertises range from epidemiology of diabetes and cardiovascular diseases in African populations to population genetics/genomics, population-based surveys and interventions. African centres also contribute existing resources and infrastructure for sample collection (clinics and field stations) and analyses. On 2015, H3A has contributed together with APCDR to fund PhD Scholarships and postdoctoral fellowships. |
| Impact | This partnership is still in its early stages. The general aim of the partnership is conduct a multi-centre population based cross-sectional survey-assessing the distribution and prevalence of a range of risk factors and quantitative phenotypes. We are currently working together to finalise the common study protocol and geographical sampling frame that will be used by all centres, enabling data from each site to combined with data from other centres for analysis. This study design provides a research framework that will allow opportunities to: 1) conduct a detailed examination of T2D and its complications; 2) assess the risk factors associated with T2D and its complications, including environmental, behavioural, infectious and genetic risk factors; 3) examine the population distribution of these risk factors; 4) harness genomic technologies to understand the aetiology of T2D and its complications in SSA; 5) provide a platform for longer-term longitudinal studies of disease incidence; and 6) develop a sustainable resource to align case series of other diseases and traits to the cross-sectional surveys. In 2015, 3x PhD studentships and 1x postdoctoral fellowship were awarded including fees, stipends and research costs. |
| Start Year | 2012 |
| Description | H3Africa Diabetes Project |
| Organisation | H3Africa |
| Country | South Africa |
| Sector | Charity/Non Profit |
| PI Contribution | Support the H3Africa Diabetes programme by enabling biomarker analysis as part of the APCDR data generation enterprise. |
| Collaborator Contribution | Participant recruitment for a case control study across 7 African countries. |
| Impact | Data generation and analysis as a means to better understand Chronic Disease prevalence in Africa. |
| Start Year | 2015 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Academy of Medical Sciences (AMS) |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Barts Health NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Cambridge University Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Central and North West London NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Charing Cross Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Chelsea and Westminster Hospital NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | East and North Hertfordshire NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Homerton University Hospital NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | King's College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | MRC/UVRI Uganda Research Unit on AIDS |
| Country | Uganda |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Clinical Trials Unit |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Human Immunology Unit |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | National Institutes of Health (NIH) |
| Department | National Institute of General Medical Sciences (NIGMS) |
| Country | United States |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Portsmouth Hospitals NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Royal Cornwall Hospitals NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | Sheffield Teaching Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | St George's Healthcare NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | St Mary's Hospital, London |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | St Richard's Hospital |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | St Thomas' Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | University College Hospital |
| Department | University College London Hospitals Charity (UCLH) |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | University of Oxford |
| Department | Wellcome Trust Centre for Human Genetics |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | HIV Genomics Consortium (HGC) |
| Organisation | West Hertfordshire Hospitals NHS Trust |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research team has started the collaboration and has designed, coordinated and delivered the 'The HIV Exome Sequencing Study: A pilot study of the genetic determinants of elite control in HIV infection'. |
| Collaborator Contribution | For 'The HIV Exome Sequencing Study' collaborating clinics identified and recruited eligible participants, collected blood samples and extracted relevant clinical data. Other partners contributed to the design of the study. |
| Impact | The specific objectives of 'The HIV Exome Sequencing Study' were as follows: 1. To conduct a pilot study to identify host and viral genetic variants that contribute to control of HIV infection. 2. To develop a research framework for large scale studies in HIV genomics. 3. To replicate findings from the study within the proposed collaboration. 4. To use fine mapping techniques to identify causal variants. 5. To develop a generic research framework to study genetic determinants of other infectious diseases. This pilot study has been completed and the data are being analysed in the context of other larger collaborations (HIV Eurocord, International HIV Acquisition Consortium (IHAC)). Other outputs of the HGC to date have been the following manuscripts: A systematic review of definitions of extreme phenotypes of HIV control and progression. Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD, Naranbhai V, Fidler S, Gkrania-Klotsas E, Post FA, Kellam P, Porter K, Sandhu MS. AIDS. 2014 Jan 14;28(2):149-62. An evaluation of HIV elite controller definitions within a large seroconverter cohort collaboration. Olson AD, Meyer L, Prins M, Thiebaut R, Gurdasani D, Guiguet M, Chaix ML, Amornkul P, Babiker A, Sandhu MS, Porter K; CASCADE Collaboration in EuroCoord. PLoS One. 2014 Jan 28;9(1):e86719 |
| Start Year | 2010 |
| Description | IAVI- Development of a transcriptomic resource for Africa |
| Organisation | International AIDS Vaccine Initiative (IAVI) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | RNA sequencing of 600 individuals across six African populations from the 1000K Genomes Project. |
| Collaborator Contribution | Provide participant samples. |
| Impact | Understanding the functional importance of these genetic variants, and the mechanisms underlying these associations requires the development of transcriptomic resources across diverse African populations, as this population-specific variation will not be represented in existing panels which are largely European in composition. |
| Start Year | 2016 |
| Description | International AIDS Vaccine Initiative (IAVI)-the Uganda Medical Informatics Center (UMIC) |
| Organisation | International AIDS Vaccine Initiative (IAVI) |
| Country | Global |
| Sector | Charity/Non Profit |
| PI Contribution | 1) Support and maintain a major high-performance computational infrastructure at MRC/UVRI Uganda-the Uganda Medical Informatics Center (UMIC) 2) Identify, train and invest in the next the generation African bioinformaticians 3) Incentivize African researchers to remain in country by developing their computational research skills 4) Utilize the MRC/UVRI data center for computationally intensive and major IAVI scientific initiatives 5) Provide an African-led computational framework to host, curate and analyse IAVI data 6) Enable data sharing across consortia, with partners, collaborators and the global scientific community |
| Collaborator Contribution | 1) Provide a data resource and platforms to promote and enable capcity building in Africa |
| Impact | Datasets from African populations are now being transfered to UMIC |
| Start Year | 2016 |
| Description | Kenya Medical Research Institute |
| Organisation | Kenyan Institute for Medical Research (KEMRI) |
| Country | Kenya |
| Sector | Public |
| PI Contribution | Provided contributions as part of the Lake Victoria Health Research Consortium |
| Collaborator Contribution | Contributed in development of research agenda for the Lake Victoria Health Research Consortium |
| Impact | We are working together in developing new proposals for funding |
| Start Year | 2013 |
| Description | NIMR Mwanza Centre |
| Organisation | National Institute for Medical Research, Tanzania |
| Department | Mwanza Intervention Trials Unit (MITU) |
| Country | Tanzania, United Republic of |
| Sector | Public |
| PI Contribution | Technical (epidemiological, statistical, clinical, research) and administrative support. |
| Collaborator Contribution | Providing laboratory and logistical infrastructure and support. |
| Impact | Strengthening research capacity in Africa; scientific publications; joint research grants |
| Description | The European Organization for Nuclear Research (CERN) |
| Organisation | European Organization for Nuclear Research (CERN) |
| Department | CERN - Other |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Seek, manage and execute the partnership agreements with CERN to secure the equipment donation, to set up a cloud based computational environment at the APCDR Uganda Medical Informatics Centre. |
| Collaborator Contribution | Agreement with CERN to donate circa £1M on computational equipment to support the expansion of the APCDR Uganda Medical Informatics Centre. |
| Impact | This collaboration has enabled the computational infrastructure necessary to set up a cloud based cluster and data base as part of the APCDR Uganda Medical Informatics Centre. This environment will host the APCDR data base, and will facilitate all projects and trainings part of the APCDR network. |
| Start Year | 2017 |
| Description | Uganda Christian University (UCU) Bioinformatics Capacity |
| Organisation | Uganda Christian University |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | Collaboration with the Uganda Christian University (UCU) to support training and development on computational biology; this will involve setting up computational infrastructure and delineating various research and education programmes to boost the profile of bioinformaticians and systems engineers in the region. |
| Collaborator Contribution | The UCU will provide the location and pre-existing educational frameworks. |
| Impact | Computational infrastructure and research and education programmes development |
| Start Year | 2018 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Armed Forces Research Institute of Medical Sciences |
| Country | Thailand |
| Sector | Public |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Foundation for the National Institutes of Health (FNIH) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Haydom Lutheran Hospital |
| Country | Tanzania, United Republic of |
| Sector | Hospitals |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) |
| Country | Bangladesh |
| Sector | Public |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Medical Research Council (MRC) |
| Department | MRC/UVRI and LSHTM Research Unit Uganda |
| Country | Uganda |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | National Centre for Research and Training on Malaria |
| Country | Burkina Faso |
| Sector | Public |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | National Institute for Medical Research, Tanzania |
| Country | Tanzania, United Republic of |
| Sector | Public |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | National Institutes of Health (NIH) |
| Department | Fogarty International Centre |
| Country | United States |
| Sector | Public |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Pontifical Catholic University of Ecuador |
| Department | Research Center for Infectious Diseases |
| Country | Ecuador |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Tribhuvan University of Nepal |
| Department | Department of Paediatrics |
| Country | Nepal |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | University of Cambridge |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | University of Oxford |
| Department | Wellcome Trust Centre for Human Genetics |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | University of Oxford |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | University of Virginia (UVa) |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | University of the Witwatersrand |
| Department | Respiratory And Meningeal Pathogens Unit |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | VaccGene - Identifying the genetic determinants of vaccine response |
| Organisation | Walter Reed Afrims Research Unit |
| Country | Nepal |
| Sector | Academic/University |
| PI Contribution | The VaccGene initiative will bring together researchers interested in genetics, immunology, infectious disease and vaccine development from around the world with the principal aim of identifying the genetic variants associated with response to multiple vaccines. We aim to perform a genome-wide association study (GWAS) using samples from approximately 10,000 infants who have received all of their vaccines in accordance with the Expanded Programme of Immunisation (EPI). My team is undertaking genotyping of samples and is providing intellectual expertise to support all subsequent analyses. It is jointly with the University of Oxford guiding the research strategy and analysis design of the study. |
| Collaborator Contribution | Jointly with our team the University of Oxford is guiding the research strategy and analysis design of the study. The other collaborators have contributes samples and data and may participate in some of the analyses. |
| Impact | Most samples have been collacted and alsyses are ongoing. |
| Start Year | 2013 |
| Description | Wellcome Trust Sanger Faculty |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have developed a large scale resource to study the aetiology of cardiometabolic traits and diseases in up to 8,000 participants from sub-Saharan Africa. |
| Collaborator Contribution | Access to analytical pipelines and sequencing anf genotyping pipelines for genomic studies. Also, provide key training for members of the team, as well as administrative, informatic and data management support for APCDR activities. |
| Impact | Genomic data on 5,000 individuals and whole genome sequencing data on 100 participants. These data will be available to the scientific community through a managed access system. APCDR data is currently handled by the Wellcome Trust Sanger Institute. Other APCDR resources such as the web site, have also been integrated within this collaborative agreement. |
| Start Year | 2010 |
| Title | Thermo Fisher/Affymetrix- Africa Array |
| Description | The use of APCDR data sets to generate a new Thermo Fisher/Affymetrix Africa Array that will enable to characterise novel, Africa-specific genetic traits and variants. |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | |
| Licensed | Yes |
| Impact | The development of the array, has enabled a highly powerful, low-cost tool to characterise Africa-specific traits, and query disease susceptibility in a systematic and reprodcible manner. |
| Description | Big data in Africa Talk-Uganda |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A talk given on behalf of APCDR, around the implications and needs of big data management in Africa. The talk helped to raise interest in the on-going works to create a Ugandan Medical Informatics Centre. A news article was published online following the talk. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.scidev.net/sub-saharan-africa/data/news/centre-launched-aid-medical-data-sharing.html |
| Description | Bioinformatics workshop (ICIPE) Nairobi, Kenya |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | A member of the Ugandan Medical Informatics Centre, under the umbrella of APCDR, attended a bioinformatics workshop at the International Center for Insect Physiology and Ecology (ICIPE) in Nairobi, Kenya themed "Bioinformatics Approaches for Next Generation Sequencing Analysis". The workshop was organized by TReND-in-Africa and run from the 30th of November to the 5th of December 2015. Its main objective was to introduce the range of bioinformatics analysis techniques for Next Generation Sequencing (NGS) data, and it was targeted at African research scientists. The participants were researchers from universities in Kenya, Nigeria, Ghana, Zambia, Uganda and a few other African countries. Our main objective at this workshop was to liaise with the key people in TReND-in-Africa to explore a potential collaboration with the organization that would have them run programs at the UMIC data centre, being then directly organised by APCDR in partnership with TReND-in-Africa. As a result of this site visit, it was agreed to run a joined workshop at UMIC in 2017, with APCDR and TReND-in-Africa acting as partners. |
| Year(s) Of Engagement Activity | 2015 |
| Description | IAVI meeting-UMIC |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presented the different capacity building activities on computational genomics that the APCDR has been fostering. |
| Year(s) Of Engagement Activity | 2016 |
| Description | MUIIplus Launch Day Talk-Uganda |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The co-director of APCDR, Dr Manjinder Sandhu, was invited to give a kaynote presentation during the first day of the MUII+ launch, to introduce the importance of the Ugandan Medical Informatics Centre (UMIC) - integrating data and computational resources to galvanise research project across the continent - and to reaffirm the long-term vision of the APCDR programme. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.muii.org.ug/data/mevents/46/MUII-PLUS-LAUNCH-DAY-ONE-.html |
| Description | Organising the Big Data for Health in Africa meeting and the Uganda Medical Informatics Centre (UMIC) official launch |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Overview This two day meeting consisted of one day of talks on the generation, implementation, analysis and visualisation and challenges of big data in the context of health research in Africa. The second day was dedicated to the launch of the Uganda Medical Informatics Centre (UMIC) which incorporated relevant presentations from the project team and directors, as well as from future user groups. Delegates In total, seventy-two delegates attend the two-day event. Delegates represented those from industry, academic, research organisations and NGOs. The nationality distribution of attendees was varied, which a large representation from East Africa accounting for over half of all delegates. |
| Year(s) Of Engagement Activity | 2016 |
| Description | UbuntuNet Alliance talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | UbuntuNet-Connect is the Annual Conference of UbuntuNet Alliance that focuses on research and education networking activities in Africa. It is organized by UbuntuNet Alliance and hosted by member NRENs. The Conference brings together practitioners in the research and education networking community, researchers, policy makers, academicians, connectivity providers, and a pool of expertise from across Africa and beyond. In previous years, the conference has attracted sponsorship from leading commercial companies and service providers. The event allowed us to showcase the Uganda Medical Informatics Centre, and stablish partnerships with members of the Network infrastructure community. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://events.ubuntunet.net/indico/event/1/ |