MRC Centre for Genomics and Global Health

Lead Research Organisation: University of Oxford
Department Name: Wellcome Trust Centre for Human Genetics

Abstract

Among the biggest challenges in medical research are (1) to develop effective vaccines against malaria, HIV/AIDS and tuberculosis, which together account for a massive global burden of disease, particularly in the developing world; (2) to combat drug resistance in malaria, HIV/AIDS, tuberculosis, enteric bacteria, invasive bacteria and other pathogens; (3) to combat the emergence of virulent pathogens such as pandemic influenza. Underlying these practical problems in global health is the biological phenomenon of genome diversity. Pathogen genomes are continually evolving in response to human immune pressure and prevailing drug usage; while at the same time infectious diseases are a major force for evolutionary selection of the human genome. Although genome diversity is a large part of the problem in infectious disease, it also offers a scientific route to understanding natural mechanisms of disease and immunity. Epidemiological analysis of the clinical consequences of pathogen genome variation may be highly informative about pathogen mechanisms of virulence, drug resistance and immune evasion. Equally, epidemiological analysis of the clinical consequences of human genome variation may be highly informative about host mechanisms of defence and protective immunity. The aim of this Translational Centre proposal is to develop the scientific environment and technical infrastructure needed to apply genomic epidemiology to practical lessons about disease prevention ? particularly about drug resistance and vaccine development.

Technical Summary

The mission of this Translational Centre is to translate state-of-the-art research on human and pathogen genome variation into large-scale clinical and epidemiological investigations of practical relevance for global health.

We will develop informatic systems and data-sharing standards to integrate clinical and epidemiological studies at the MRC Laboratories in The Gambia, the KEMRI/Wellcome Unit in Kenya and the Wellcome Units in Vietnam and Thailand, with high-throughput genome technologies, bioinformatics and statistical genetics at Oxford University and the Sanger Institute.

We will use these systems to accelerate vaccine development and to tackle drug resistance in malaria by investigating the clinical and biological consequences of variations in the human genome and in the Plasmodium falciparum genome in malaria-exposed populations.

The systems and tools that we develop will also support genome research on other diseases that are being investigated in the Gambian, Kenyan, Vietnamese and Thai units, including influenza, enteric bacteria, tuberculosis, HIV/AIDS, dengue, chlamydia, bacterial meningitis and pneumococcal disease.

Organisations

Publications

10 25 50
publication icon
Almagro-Garcia J (2009) SnoopCGH: software for visualizing comparative genomic hybridization data. in Bioinformatics (Oxford, England)

publication icon
Anopheles Gambiae 1000 Genomes Consortium (2017) Genetic diversity of the African malaria vector Anopheles gambiae. in Nature

 
Description Convened meeting with malaria control programme / public health leaders on the integration of genetic information into national malaria control programme decision making to accelerate malaria control and elimination efforts.
Geographic Reach Asia 
Policy Influence Type Participation in a advisory committee
 
Description BMGF Global Health Award
Amount $2,994,801 (USD)
Funding ID OPP1040463 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 11/2011 
End 07/2014
 
Description Global Health Program
Amount $4,800,000 (USD)
Funding ID OPP1118166 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 01/2015 
End 10/2017
 
Description MRC Centenary Award
Amount £105,000 (GBP)
Funding ID G0600718/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 03/2012 
End 09/2013
 
Description MRC Centre Directors Capital Fund
Amount £150,000 (GBP)
Organisation Medical Research Council (MRC) 
Department MRC National Institute for Medical Research (NIMR)
Sector Public
Country United Kingdom
Start 03/2013 
End 09/2014
 
Description MRC Research Grant
Amount £1,956,764 (GBP)
Funding ID MR/M006212/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 01/2015 
End 01/2018
 
Description Wellcome Trust Strategic Award
Amount £6,000,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2010 
End 11/2015
 
Description Worldwide Antimalarial Resistance Network
Amount £1,750,000 (GBP)
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start  
 
Title E learning - Ethics Committees Reviewing Genomic Research 
Description This is a specialist e-learning course for committees reviewing research at the FERCAP Conference in November 2012. The course focuses on ethical issues in genomic research. 
Type Of Material Improvements to research infrastructure 
Year Produced 2012 
Provided To Others? Yes  
Impact This course is openly available through the Global Health Trails website (http://globalhealthtrials.tghn.org/) and forms part of a suite of e-learning courses of relevance to global health. 
URL http://globalhealthtrials.tghn.org/
 
Title High throughput genotyping methods 
Description We have developed and implemented mass-spec based methods for cost-effective SNP genotyping of 10,000's of samples from poor-quality samples from multicentre studies in Africa. 
Type Of Material Technology assay or reagent 
Year Produced 2007 
Provided To Others? Yes  
Impact It has allowed us to provide genetic data on >100,000 samples for partners in >20 countries 
 
Title MapSeq 
Description MapSeq is a web-based application designed to link deep genome sequencing to epidemiology, allowing exploration of genetic variation data in the context of geographical distributions and other phenotypic associations. MapSeq stores and manages genomic data from large numbers of samples, and presents this data in forms that make it easier to discern patterns and explore hypotheses. 
Type Of Material Improvements to research infrastructure 
Year Produced 2009 
Provided To Others? Yes  
Impact See www.mapseq.net/pf Featured in WIRED, Scientific American. 
URL http://www.mapseq.net/pf
 
Title Panoptes 
Description Panoptes is an open source software framework for collaborative visual exploration of large scale genome variation data and associated metadata in a web browser. It can be used to browse large, hybrid data sets in a coherent and user friendly way, and offers interactive visual analytics tools to assist the exploration. 
Type Of Material Improvements to research infrastructure 
Year Produced 2014 
Provided To Others? Yes  
Impact Example deployment: http://www.malariagen.net/apps/pf3k 
URL https://github.com/cggh/panoptes
 
Title Ag1000G phase 1 AR3.1 data release 
Description First released in December 2016, the AR3.1 data release represented the full data release of Phase 1 of the Ag1000g project. Comprising 845 mosquito specimens in total it included haplotype data available as either VCF, HDF5 or Zarr format files, and other associated data files. It also includes results from various population genomic analyses and SNP validation experiments. In November 2017 this dataset was expanded (phase 2 AR1) to genome-wide variant calls, haplotypes and associated data for 1,142 wild-caught specimens collected from 13 countries spanning sub-Saharan Africa, and 234 specimens comprising parents and progeny of 11 lab crosses. All mosquitoes were sequenced by the Wellcome Trust Sanger Institute's Malaria programme as part of the Ag1000g project. CGGH supported the process of data management, software engineering, data visualisation and analysis.The datasets are available https://www.malariagen.net/data/ag1000g-phase1-ar3.1 and https://www.malariagen.net/data/ag1000g-phase-2-ar1 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This large data release provides the scientific community with a fantastic resource to investigate a huge variety of questions on a number of topics, such as speciation genomics, evidence for selection, and levels of population diversity. An example is a recent publication in Nature of the largest study of Anopheles genome variation, providing new tools to monitor and manage insecticide resistance and to design effective targets for gene drive strategies for vector control. 
URL https://www.malariagen.net/data/ag1000g-phase1-ar3.1
 
Title P. falciparum genomic data 
Description A longstanding commitment to generating whole genome sequence data on malaria parasites has resulted in several large datasets on human malaria parasites - both falciparum and vivax. All parasites were sequenced by the Wellcome Trust Sanger Institute's Malaria programme as part of the MalariaGEN Pf Community Project or P. vivax Genome Variation Project. In 2017 these data, on nearly 4000 parasites, became entirely open access. CGGH supported the process of data management, software engineering, data visualisation and analysis. CGGH also coordinated the Pf3k project whereby almost 2500 samples of these data, together with other openly available falciparum sequencing data were analysed to undertake a comprehensive analysis of genome variation in 3,000 parasite samples representing the major malaria endemic regions of the world. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This large data release provides the scientific community with a fantastic resource to investigate a huge variety of questions on a number of topics, such as genome variation, population genetics and evolutionary selection. An example is a recent publication in Lancet Infectious diseases of the most comprehensive genetic study of malaria parasites in Southeast Asia which showed that resistance to antimalarial drugs was under-reported for years in Cambodia. It revealed that resistance to the combination therapy appeared almost as soon as that treatment was introduced as the official first line therapy and that it spread steadily and aggressively after that. It also showed that it is now possible to use modern genomic technologies to get a fuller picture of a malaria outbreak. 
URL https://www.malariagen.net/data/p-falciparum-community-project-jan-2016-data-release
 
Description Local capacity in West Africa for genomic surveillance of malaria parasites and vectors 
Organisation Medical Research Council (MRC)
Department MRC Unit, The Gambia
Country Gambia 
Sector Public 
PI Contribution Drug and insecticide resistance are roadblocks to sustainable malaria control in Africa. It is essential that national malaria control programmes (NMCPs) have effective tools to monitor resistance, both to know what are the best drugs and insecticides to use, and also to provide early warning that their interventions are causing resistance to rise to dangerous levels, indicating the need for a change in strategy. However current methods of monitoring drug and insecticide resistance are cumbersome, time consuming and not always accurate. There are many technical challenges in getting this to work for malaria parasites and mosquitoes, but we now have proof of concept in our UK research lab and we are now working with two research partners to start putting these systems in place in Africa. We will establish laboratory and computational systems for genomic surveillance of malaria at the University of Ghana in Accra and the MRC Unit in The Gambia. These two sites have been selected because of their excellent laboratory infrastructure, their critical mass of scientific expertise, their strong links with NMCPs, and the many different challenges for malaria control in the two locations. Once the technical systems are in place, we will work with local partners to optimise the pipeline for reliability, scalability and cost-effectiveness, and to learn how to integrate it most effectively into NMCP operations. We aim to learn how to translate genomic data into actionable knowledge, e.g. by providing early warning of newly emerging resistance, and by showing how specific interventions are causing levels of resistance to rise or fall. By the end of this project, we aim to have sufficient proof of concept to start integrating these systems into the routine working practices of NMCPs in Ghana and The Gambia, and to provide a working example of how such systems could be deployed at other locations in Africa.
Collaborator Contribution This partnership has outstanding local leadership and institutional support at both locations. At the Institutional level, Profs. Awandare and d'Alessandro are both renowned malaria experts. The two project leads based is Africa, Drs. Amambua Ngwa and Amenga-Etego, are among the most technically accomplished African researchers working in the field of malaria population genetics, with significant experience in epidemiological, laboratory and analytical aspects of proposed work.
Impact Approx £2m in funding has been awarded for this work in principle. This will be reflected in the 2019 Research Fish Submission.
Start Year 2017
 
Description Local capacity in West Africa for genomic surveillance of malaria parasites and vectors 
Organisation University of Accra
Country Ghana 
Sector Academic/University 
PI Contribution Drug and insecticide resistance are roadblocks to sustainable malaria control in Africa. It is essential that national malaria control programmes (NMCPs) have effective tools to monitor resistance, both to know what are the best drugs and insecticides to use, and also to provide early warning that their interventions are causing resistance to rise to dangerous levels, indicating the need for a change in strategy. However current methods of monitoring drug and insecticide resistance are cumbersome, time consuming and not always accurate. There are many technical challenges in getting this to work for malaria parasites and mosquitoes, but we now have proof of concept in our UK research lab and we are now working with two research partners to start putting these systems in place in Africa. We will establish laboratory and computational systems for genomic surveillance of malaria at the University of Ghana in Accra and the MRC Unit in The Gambia. These two sites have been selected because of their excellent laboratory infrastructure, their critical mass of scientific expertise, their strong links with NMCPs, and the many different challenges for malaria control in the two locations. Once the technical systems are in place, we will work with local partners to optimise the pipeline for reliability, scalability and cost-effectiveness, and to learn how to integrate it most effectively into NMCP operations. We aim to learn how to translate genomic data into actionable knowledge, e.g. by providing early warning of newly emerging resistance, and by showing how specific interventions are causing levels of resistance to rise or fall. By the end of this project, we aim to have sufficient proof of concept to start integrating these systems into the routine working practices of NMCPs in Ghana and The Gambia, and to provide a working example of how such systems could be deployed at other locations in Africa.
Collaborator Contribution This partnership has outstanding local leadership and institutional support at both locations. At the Institutional level, Profs. Awandare and d'Alessandro are both renowned malaria experts. The two project leads based is Africa, Drs. Amambua Ngwa and Amenga-Etego, are among the most technically accomplished African researchers working in the field of malaria population genetics, with significant experience in epidemiological, laboratory and analytical aspects of proposed work.
Impact Approx £2m in funding has been awarded for this work in principle. This will be reflected in the 2019 Research Fish Submission.
Start Year 2017
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Institute for Endemic Diseases IEND
Country Sudan 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Kwame Nkrumah University of Science and Technology (KNUST)
Country Ghana 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Liverpool School of Tropical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Country United Kingdom 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation MURAZ Center
Country Burkina Faso 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Mahidol University
Country Thailand 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Medical Research Council (MRC)
Department MRC Unit, The Gambia
Country Gambia 
Sector Public 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation National Institute for Medical Research, Tanzania
Country Tanzania, United Republic of 
Sector Public 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Noguchi Memorial Institute for Medical Research (NMRR)
Country Ghana 
Sector Learned Society 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Papua New Guinea Institute of Medical Research
Country Papua New Guinea 
Sector Public 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Pasteur Institute Dakar
Country Senegal 
Sector Charity/Non Profit 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Pasteur Institute, Paris
Country France 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Sapienza University of Rome
Department Parasitology Sapienza
Country Italy 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Stockholm University
Country Sweden 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Bamako
Department Malaria Research and Training Centre (MRTC) Bamako
Country Mali 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Buea
Country Cameroon 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Colombo
Department Department of Parasitology
Country Sri Lanka 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Malawi
Country Malawi 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Maryland
Department Centre for Vaccine Development (CVD)
Country United States 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Michigan
Country United States 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation University of Oxford
Department Oxford University Clinical Research Unit Vietnam (OUCRU)
Country Viet Nam 
Sector Academic/University 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description Malaria Genomic Epidemiology Network (MalariaGEN) 
Organisation Wellcome Trust
Department KEMRI-Wellcome Trust Research Programme
Country Kenya 
Sector Multiple 
PI Contribution I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
 
Description PAMGEM 
Organisation Addis Ababa University
Country Ethiopia 
Sector Academic/University 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation Kenyan Institute for Medical Research (KEMRI)
Country Kenya 
Sector Public 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation Medical Research Council (MRC)
Department MRC Unit, The Gambia
Country Gambia 
Sector Public 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation Pasteur Institute of Madagascar
Country Madagascar 
Sector Charity/Non Profit 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation University of Bamako
Department Malaria Research and Training Centre (MRTC) Bamako
Country Mali 
Sector Academic/University 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description PAMGEM 
Organisation University of Buea
Country Cameroon 
Sector Academic/University 
PI Contribution The Pan-African Malaria Genetic Epidemiology Network (PAMGEN) is a robust network of African scientists - within and outside Africa- working in collaboration with leading researchers around the world, to use the latest genetics and genomics science to contribute towards efforts at malaria elimination in Africa. Recently funded by the H3 Africa Initiative, PAMGEM is a natural evolution of the Centre for Genomics and Global Health capacity building activities. Several of the lead applicants have a longstanding involvement in CGGH and have received training, mentorship and practical support through it the bursary scheme supported by the MRC Centenary award, data clinics and advanced training workshops. We are supporting this initiative in various ways and our overarching goal is to support this team of African scientists to harness advanced genomic and computational technologies to better understand how variation in human, parasite and mosquito genomes, as well as in the ecological environment, impact on malaria at individuals and population level. This will involve supporting the establishment of an appropriate governance structure and project management support, technical support for genotyping and genome sequencing in country, data management and processing and the visualisation of their data through CGGH developed web interfaces.
Collaborator Contribution PAMGEM will be led by African scientists, placing them at the centre of international research efforts to find sustainable ways to drive down the huge burden of malaria in Africa. Specifically, they will focus on the genetic interactions between human populations and malaria parasites in different environmental settings across Africa.
Impact The partnership has resulted in funding of $3m for PAMGEM.
Start Year 2017
 
Description Plasmodium Diversity Network Africa 
Organisation Addis Ababa University
Department Aklilu Lemma Institute of Pathobiology
Country Ethiopia 
Sector Academic/University 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Congo National Institute of Biomedical Research
Country Congo, the Democratic Republic of the 
Sector Public 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Cote D'Ivoire's National Institute of Public Health
Department Malaria Research and Control Centre
Country Cote d'Ivoire 
Sector Public 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Medical Research Council (MRC)
Department MRC Unit, The Gambia
Country Gambia 
Sector Public 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation National Institute for Medical Research, Tanzania
Department NIMR Mbeya Research Centre
Country Tanzania, United Republic of 
Sector Public 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Navrongo Health Research Centre (NHRC)
Country Ghana 
Sector Public 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Noguchi Memorial Institute for Medical Research (NMRR)
Country Ghana 
Sector Learned Society 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation Pasteur Institute of Madagascar
Country Madagascar 
Sector Charity/Non Profit 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation University of Bamako
Department Malaria Research and Training Centre (MRTC) Bamako
Country Mali 
Sector Academic/University 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation University of Buea
Department Department of Biochemistry and Microbiology
Country Cameroon 
Sector Academic/University 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Plasmodium Diversity Network Africa 
Organisation University of Health Sciences, Gabon
Country Gabon 
Sector Academic/University 
PI Contribution CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year 2013
 
Description Tracking Resistance to Artemisinin Collaboration 
Organisation Wellcome Trust
Department Mahidol University-Oxford Tropical Medicine Research Programme
Country Thailand 
Sector Academic/University 
PI Contribution The TRAC (Tracking Resistance to Artemisinins Collaboration) study is coordinating prospective clinical and parasitological studies to assess artemisinin susceptibility in 1500 patients in 15 sites across Asia and Africa. This series of studies will provide well characterized malaria parasites with defined parasite clearance profiles for laboratory and molecular characterization, giving us a unique opportunity to identify a molecular marker of artemisinin resistance and validate an accurate laboratory test to detect resistance. The MRC Centre for Genomics and Global Health is supporting TRAC to perform a genome-wide association study of genetic correlates of delayed parasite clearance, based on genome sequencing of parasites in clinical samples. Initial work is focusing on establishing systems to manage the hundreds of terabytes of raw sequence data generated by this project. Also implementing a process of discovering and validating novel SNPs and other forms of genome variation in these samples, primarily based on alignment to the P.falciparum reference genome but also employing new methods of de-novo genome assembly that are currently under development. Having constructed a comprehensive catalogue of both novel and previously-reported variants, we will carry out genotyping of each sample, using statistical methods for quality assurance that have been validated using independent benchmarks. Having determined genotypes for each sample, we will carry out analyses of genetic association with the clinical phenotype. The aim of this project is that the results will be shared with the research community through user-friendly web tools that will allow scientists and public health authorities to navigate the massive quantities of information generated by the TRAC project.
Collaborator Contribution see above
Impact This project is at an early stage. We have already released genome sequence data on 1000 P. falciparum samples.
Start Year 2011
 
Description UKCRC Modernising Medical Microbiology consortium 
Organisation Oxford University Hospitals NHS Foundation Trust
Country United Kingdom 
Sector Public 
PI Contribution We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution See above
Impact Web application is in development
Start Year 2009
 
Description UKCRC Modernising Medical Microbiology consortium 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution See above
Impact Web application is in development
Start Year 2009
 
Description UKCRC Modernising Medical Microbiology consortium 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution See above
Impact Web application is in development
Start Year 2009
 
Description UKCRC Modernising Medical Microbiology consortium 
Organisation University of Oxford
Department Nuffield Department of Clinical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution See above
Impact Web application is in development
Start Year 2009
 
Description Wellcome Trust Sanger Institute 
Organisation The Wellcome Trust Sanger Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution As head of the Malaria Programme and the Global Health Strategy Group at the Sanger Institute, I'm engaged in all levels of work - scientific, strategic and operational.
Collaborator Contribution The Sanger Institute provides infrastructure, resources and expertise in large-scale genome sequencing, genome-wide SNP typing, informatics and functional genomics.
Impact Examples relevant to this grant: 1. The world's largest repository of DNA samples and clinical data for genetic studies of host-parasite interactions in malaria 2. Publication of the first genome-wide association study of human disease susceptibility in Africa 3. A large multicentre case-control study of severe malaria, representing the largest ongoing genome-wide association study of an infectious disease. In December 2011 we completed genotyping of >1 million SNPs on >20,000 individuals from 10 different populations.
Start Year 2006
 
Description WorldWide Antimalarial Resistance Network 
Organisation Menzies School of Health Research
Country Australia 
Sector Academic/University 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description WorldWide Antimalarial Resistance Network 
Organisation University of Cape Town
Country South Africa 
Sector Academic/University 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description WorldWide Antimalarial Resistance Network 
Organisation University of Maryland
Country United States 
Sector Academic/University 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description WorldWide Antimalarial Resistance Network 
Organisation University of Oxford
Department Nuffield Department of Clinical Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description WorldWide Antimalarial Resistance Network 
Organisation University of Washington
Country United States 
Sector Academic/University 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description WorldWide Antimalarial Resistance Network 
Organisation World Health Organization (WHO)
Country Global 
Sector Public 
PI Contribution As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year 2008
 
Description Cambodia Manuscript Press Release 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact A press release and associated follow up interviews led to media coverage of 64 stories in 13 languages (mostly in English, 78%); National coverage in 23 countries; High-profile coverage included Wired UK, BBC, The Guardian, FoxNews, AFP. Coverage on twitter included 12 tweets from accounts such as BBC World Service, Times of India, and Agence France Presse reached a combined following of 1.3 million users.

see above
Year(s) Of Engagement Activity 2013
 
Description Genetic diversity of the African malaria vector Anopheles gambiae 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release for Nature publication
Year(s) Of Engagement Activity 2017
URL https://www.malariagen.net/news-events/press-release/largest-genetic-study-mosquitoes-reveals-spread...
 
Description Integration of genetic epidemiology into malaria control decision making - Use Cases Working Group Meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact Working group meeting with representatives from Laos, Cambodia, Thailand, Vietnam and Myanmar to discuss use cases for innovative surveillance methods and tools used to guide decision-making and operations in Greater Mekong Sub-region by 2020.
Year(s) Of Engagement Activity 2018
 
Description Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release The Lancet Infectious Diseases publication
Year(s) Of Engagement Activity 2018
URL https://www.malariagen.net/news-events/press-release/multidrug-resistant-malaria-spread-under-radar-...
 
Description Radio 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact BBC World Service "The Age of the Genome". Kwiatkowski interviewed by Richard Dawkins.

further media inquiries
Year(s) Of Engagement Activity 2010
 
Description Resistance to malaria through structural variation of red blood cell invasion receptors 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release for Science publication
Year(s) Of Engagement Activity 2017
URL https://www.malariagen.net/news-events/press-release/natural-resistance-malaria-linked-variation-hum...
 
Description Various articles in popular media 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our work has been featured in articles and news items in WIRED, Prospect and Scientific American

further media inquiries
Year(s) Of Engagement Activity 2009,2010
 
Description WHO meeting on Pathogen Genome Sequence Data Sharing During Public Health Emergencies 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Participated in WHO Research and Development Blueprint meeting on Pathogen Genome Sequence Data Sharing During Public Health Emergencies
Year(s) Of Engagement Activity 2017