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.

Funded Value:

£3,115,095

Funded Period:

Mar 08 - Oct 14

Funder:

MRC

Project Status:

Closed

Project Category:

Research Grant

Project Reference:

G0600718

Principal Investigator:

Dominic Peter Kwiatkowski

Health Category:

Infection (100%)

Research Activity:

1.4 Methodologies and measurements (34%)

2.1 Biological and endogenous factors (33%)

5.1 Pharmaceuticals (33%)

Organisations

People	ORCID iD
Dominic Peter Kwiatkowski (Principal Investigator)

Publications

Author Name

Title Publication Date Published

|< < 1 2 3 4 5 6 7 8 9 10 > >|

10 25 50

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 Plasmodium falciparum 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

Ansbro MR (2020) Development of copy number assays for detection and surveillance of piperaquine resistance associated plasmepsin 2/3 copy number variation in Plasmodium falciparum. 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

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

Ariey F (2014) A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. in Nature

Policy Influence
Further Funding
Research Databases and Models
Research Tools and Methods
Collaboration
Engagement Activities


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	Public
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	Academic/University
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	Public
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 (updated 2021)
Organisation	Medical Research Council (MRC)
Department	MRC Unit, The Gambia
Country	Gambia
Sector	Public
PI Contribution	The NIHR Global Health Research Group on genomic surveillance of malaria in West Africa is a UK Government funded-project to establish local capacity in West Africa for genomic surveillance of malaria parasites and vectors, and to develop analytical outputs that will be of practical value to National Malaria Control Programmes in planning effective interventions in the face of increasing drug and insecticide resistance. Partners are MRC Gambia and WACCBIP (University of Ghana) and the Wellcome Sanger Institute. In the past year we have achieved a working proof of concept for genomic surveillance of malaria parasites and vectors in Ghana and The Gambia, and are beginning the process of establishing a framework for expanding the scope of such surveillance systems to regional (or continental) scales. Dr Ngwa in Gambia has agreements in place to support Senegal, Sierra Leone, Nigeria and Guinea. Prof Awandare and Dr Amenga-Etego have agreement to support Burkina Faso and Nigeria.
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. Expertise developed through this activity has been applied to COVID-19 amplicon sequencing undertaken in Ghana.
Start Year	2017


Description	Local capacity in West Africa for genomic surveillance of malaria parasites and vectors (updated 2021)
Organisation	University of Accra
Country	Ghana
Sector	Academic/University
PI Contribution	The NIHR Global Health Research Group on genomic surveillance of malaria in West Africa is a UK Government funded-project to establish local capacity in West Africa for genomic surveillance of malaria parasites and vectors, and to develop analytical outputs that will be of practical value to National Malaria Control Programmes in planning effective interventions in the face of increasing drug and insecticide resistance. Partners are MRC Gambia and WACCBIP (University of Ghana) and the Wellcome Sanger Institute. In the past year we have achieved a working proof of concept for genomic surveillance of malaria parasites and vectors in Ghana and The Gambia, and are beginning the process of establishing a framework for expanding the scope of such surveillance systems to regional (or continental) scales. Dr Ngwa in Gambia has agreements in place to support Senegal, Sierra Leone, Nigeria and Guinea. Prof Awandare and Dr Amenga-Etego have agreement to support Burkina Faso and Nigeria.
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. Expertise developed through this activity has been applied to COVID-19 amplicon sequencing undertaken in Ghana.
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	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	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	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	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	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	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. 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 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. 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 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. 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 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	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. 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 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. 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 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. 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 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. 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 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	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	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	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	Navrongo Health Research Centre (NHRC)
Country	Ghana
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	Noguchi Memorial Institute for Medical Research (NMRR)
Country	Ghana
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	Pasteur Institute of Madagascar
Country	Madagascar
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 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	United Kingdom
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	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	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

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