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.
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
- University of Oxford, United Kingdom (Collaboration, Lead Research Organisation)
- University of Colombo, Sri Lanka (Collaboration)
- Public Health England, United Kingdom (Collaboration)
- Kwame Nkruma University of Science & Tec (Collaboration)
- University of Cape Town (Collaboration)
- Pasteur Institute Dakar (Collaboration)
- Addis Ababa University, Ethiopia (Collaboration)
- University of Rome I (La Sapienza), Italy (Collaboration)
- Noguchi Memorial Inst for Medical Res (Collaboration)
- University of Malawi, Malawi (Collaboration)
- Papua New Guinea Inst of Med Research (Collaboration)
- Pasteur Institute, Paris (Collaboration)
- Cote D'Ivoire's National Institute of Public Health (Collaboration)
- University of Maryland, United States (Collaboration)
- University of Buea, Cameroon (Collaboration)
- Pasteur Institute of Madagascar (Collaboration)
- Menzies School of Health Research (Collaboration)
- National Institute for Medical Research (Collaboration)
- Washington University in St. Louis (Collaboration)
- Institute for Endemic Diseases IEND (Collaboration)
- Oxford University Hospitals NHS Trust, United Kingdom (Collaboration)
- London Sch of Hygiene and Trop Medicine, United Kingdom (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration)
- World Health Organization (WHO) (Collaboration)
- Medical Research Council (Collaboration)
- University of Health Sciences, Gabon (Collaboration)
- University of Michigan, United States (Collaboration)
- Mahidol University (Collaboration)
- University of Accra (Collaboration)
- University of Bamako (Collaboration)
- Congo National Institute of Biomedical Research (Collaboration)
- Wellcome Trust, LONDON (Collaboration)
- Kenyan Institute for Medical Research (KEMRI) (Collaboration)
- Navrongo Health Research Centre (NHRC) (Collaboration)
- MURAZ Center (Collaboration)
- University of Stockholm (Collaboration)
- Liverpool School of Tropical Medicine (Collaboration)
People |
ORCID iD |
| Dominic Peter Kwiatkowski (Principal Investigator) |
Publications
Almagro-Garcia J
(2009)
SnoopCGH: software for visualizing comparative genomic hybridization data.
in Bioinformatics (Oxford, England)
Amambua-Ngwa A
(2012)
Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.
in PLoS genetics
Amambua-Ngwa A
(2019)
Major subpopulations of in sub-Saharan Africa.
in Science (New York, N.Y.)
Amato R
(2017)
Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium falciparum malaria in Cambodia: a genotype-phenotype association study.
in The Lancet. Infectious diseases
Amato R
(2018)
Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study.
in The Lancet. Infectious diseases
Anopheles Gambiae 1000 Genomes Consortium
(2017)
Genetic diversity of the African malaria vector Anopheles gambiae.
in Nature
Apinjoh TO
(2014)
Association of candidate gene polymorphisms and TGF-beta/IL-10 levels with malaria in three regions of Cameroon: a case-control study.
in Malaria journal
Apinjoh TO
(2013)
Association of cytokine and Toll-like receptor gene polymorphisms with severe malaria in three regions of Cameroon.
in PloS one
Ariey F
(2014)
A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.
in Nature
Auburn S
(2012)
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
in PloS one
| 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 |