Research partnership to assess the burden and aetiology of non-communicable diseases (NCDs) in sub-Saharan Africa (SSA)

Lead Research Organisation: University of Cambridge
Department Name: Public Health and Primary Care

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.

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.

Organisations

Publications

10 25 50
publication icon
Allcock S (2017) Antimicrobial resistance in human populations: challenges and opportunities. in Global health, epidemiology and genomics

publication icon
Allcock SH (2019) Sociodemographic patterns of health insurance coverage in Namibia. in International journal for equity in health

publication icon
Barr AL (2016) The need for an integrated approach for chronic disease research and care in Africa. in Global health, epidemiology and genomics

 
Description IAVI/UMIC collaboration agreement
Amount £623,682 (GBP)
Organisation United States Agency for International Development 
Sector Public
Country United States
Start 07/2016 
End 07/2021
 
Description Medical bioinformatics strategic award
Amount £2,830,000 (GBP)
Funding ID MR/L016273/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
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
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 Medical Research Council (MRC), MRC/UVRI Unit, Uganda
Country Uganda 
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 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 Multiple 
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 Hospitals 
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 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
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 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 Society for Bioinformatics and Computational Biology (ASBCB) 
Organisation African Society for Bioinformatics and Computational Biology
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 Private 
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 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 EuroCoord Network of Excellence 
Organisation 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 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 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 Institute of Development Research (IRD)
Country France 
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 International Centre for Research and Development of Livestock in Subhumid (CIRDES)
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 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 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 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 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 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 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 H3Africa Diabetes Project 
Organisation H3Africa
Country United States 
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 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 Human Immunology Unit
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 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 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 St Richard's Hospital
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 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 London 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 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 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
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 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 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 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 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 Medical Research Council (MRC), MRC/UVRI Unit, Uganda
Country Uganda 
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 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 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 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
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/