Host determinants of malarial pathogenesis [Professorship award]

Lead Research Organisation: University of Oxford

Department Name: Paediatrics

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Host determinants of malarial pathogenesis

Funded Value:

£810,523

Funded Period:

Oct 98 - Sep 11

Funder:

MRC

Project Status:

Closed

Project Category:

Fellowship

Project Reference:

G19/9

Principal Investigator:

Dominic Peter Kwiatkowski

Health Category:

Infection (200%)

Research Activity:

2.1 Biological and endogenous factors (200%)

Organisations

People	ORCID iD
Dominic Peter Kwiatkowski (Principal Investigator / Fellow)

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

Atkinson SH (2006) Seasonal childhood anaemia in West Africa is associated with the haptoglobin 2-2 genotype. in PLoS medicine

Atkinson SH (2008) Tumor necrosis factor SNP haplotypes are associated with iron deficiency anemia in West African children. in Blood

Auburn S (2012) Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data. in PloS one

Auburn S (2011) An effective method to purify Plasmodium falciparum DNA directly from clinical blood samples for whole genome high-throughput sequencing. in PloS one

Auburn S (2008) Association of the GNAS locus with severe malaria. in Human genetics

Auburn S (2010) Further evidence supporting a role for gs signal transduction in severe malaria pathogenesis. in PloS one

Auburn S (2013) Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing. in PloS one

Band G (2013) Imputation-based meta-analysis of severe malaria in three African populations. in PLoS genetics

Policy Influence
Further Funding
Research Tools and Methods
Collaboration
Engagement Activities


Description	Advanced courses in genomic epidemiology
Geographic Reach	Multiple continents/international
Policy Influence Type	Influenced training of practitioners or researchers


Description	Head of Informatics, Worldwide Antimalarial Resistance Network
Geographic Reach	Multiple continents/international
Policy Influence Type	Participation in advisory committee


Description	MalariaGEN Data Fellowship scheme
Geographic Reach	Multiple continents/international
Policy Influence Type	Influenced training of practitioners or researchers


Description	MalariaGEN policies for data sharing
Geographic Reach	Multiple continents/international
Policy Influence Type	Citation in other policy documents


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	Grand Challenges in Global Health initiative
Amount	£6,000,000 (GBP)
Organisation	Bill and Melinda Gates Foundation
Sector	Charity/Non Profit
Country	United States
Start	09/2005
End	06/2013


Description	Grand Challenges in Global Health initiative
Amount	£6,000,000 (GBP)
Organisation	Wellcome Trust
Sector	Charity/Non Profit
Country	United Kingdom
Start	09/2005
End	06/2010


Description	MRC Programme Grant
Amount	£1,500,000 (GBP)
Organisation	Medical Research Council (MRC)
Sector	Academic/University
Country	United Kingdom
Start	09/2006
End	03/2011


Description	Wellcome Trust Sanger Institute Malaria Programme
Amount	£10,000,000 (GBP)
Organisation	Wellcome Trust
Sector	Charity/Non Profit
Country	United Kingdom
Start	09/2011
End	09/2016


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


Title	ExplorerCat
Description	ExplorerCat is a user-friendly web application that allows researchers without informatics skills to query and browse complex population genomic databases, e.g. to search through large catalogues of genetic variants for those with high levels of population differentiation or haplotypic signatures of recent positive selection. See http://www.sanger.ac.uk/MapSeqExplorerCat/
Type Of Material	Improvements to research infrastructure
Year Produced	2010
Provided To Others?	Yes
Impact	ExplorerCat has been used to release the first global survey of regional allele frequencies for ~100,000 SNPs in the Plasmodium falciparum genome.
URL	http://www.sanger.ac.uk/MapSeqExplorerCat/


Title	Genomewide association studies of malaria in The Gambia, Ghana and Malawi
Description	Data submitted to European Genotyping Archive. Any bona fide researcher may apply for access via an Independent Data Access committee.
Type Of Material	Biological samples
Year Produced	2009
Provided To Others?	Yes
Impact	First genomewide association study performed in Africa. Papers in Nature Genetics and Nature Reviews Genetics. Development of an ethical policy for GWAS data release, in consultation with stakeholders in developing countries, published in Nature and PLoS Medicine.


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	Illuminus
Description	Genotype calling algorithm for genome-wide SNP typing, published in Bioinformatics and available as open source software
Type Of Material	Improvements to research infrastructure
Year Produced	2008
Provided To Others?	Yes
Impact	Over the past 3 years, Illuminus has been one of the most popular genotype-calling algorithms used in GWAS studies.


Title	LookSeq
Description	An interactive web viewer for browsing large volumes of next-generation sequencing data, published in Genome Research and released as open-source software.
Type Of Material	Improvements to research infrastructure
Year Produced	2009
Provided To Others?	Yes
Impact	We developed LookSeq initially for the malaria research community. It has been adopted and adapted by the Mouse Genome sequencing community and other groups.


Title	MalariaGEN Consortial Resource
Description	A repository of >100,000 DNA samples with detailed clinical data, collected by researchers in over 20 malaria endemic countries, for global multicentre studies of human resistance to malaria, parasite resistance to anti-malarial drugs, and mosquito resistance to insecticides.
Type Of Material	Biological samples
Provided To Others?	No
Impact	Development of ethical policies and procedures for global data-sharing networks involving rich and poor countries (published in Nature and elsewhere); GWAS studies of >20,000 individuals (published in Nature Genetics and work in progress); a capacity-building initiative that has trained researchers in 16 malaria endemic countries in data analysis & statistics.


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	SnoopCGH
Description	Web-based visualization of comparative genome hybridisation data, published in Bioinformatics and available as open-source software.
Type Of Material	Improvements to research infrastructure
Year Produced	2009
Provided To Others?	Yes
Impact	-


Title	Web applications for a global data-sharing network
Description	User-friendly web applications for sharing large and datasets between researchers in rich and poor countries.
Type Of Material	Improvements to research infrastructure
Year Produced	2006
Provided To Others?	Yes
Impact	Underpins MalariaGEN data-sharing network


Title	Web applications for genomic epidemiology
Description	User-friendly web applications for browsing and querying large genetic epidemiology databases
Type Of Material	Improvements to research infrastructure
Year Produced	2006
Provided To Others?	Yes
Impact	Underpins the MalariaGEN data-sharing network


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Institute for Endemic Diseases IEND
Country	Sudan
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Kwame Nkrumah University of Science and Technology (KNUST)
Country	Ghana
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Liverpool School of Tropical Medicine
Country	United Kingdom
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	London School of Hygiene and Tropical Medicine (LSHTM)
Country	United Kingdom
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	MURAZ Center
Country	Burkina Faso
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Mahidol University
Country	Thailand
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Medical Research Council (MRC)
Department	MRC Unit, The Gambia
Country	Gambia
Sector	Public
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	National Institute for Medical Research, Tanzania
Country	Tanzania, United Republic of
Sector	Public
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Noguchi Memorial Institute for Medical Research (NMRR)
Country	Ghana
Sector	Learned Society
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Papua New Guinea Institute of Medical Research
Country	Papua New Guinea
Sector	Public
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Pasteur Institute Dakar
Country	Senegal
Sector	Charity/Non Profit
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Pasteur Institute, Paris
Country	France
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Sapienza University of Rome
Department	Parasitology Sapienza
Country	Italy
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Stockholm University
Country	Sweden
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	The Wellcome Trust Sanger Institute
Country	United Kingdom
Sector	Charity/Non Profit
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Bamako
Department	Malaria Research and Training Centre (MRTC) Bamako
Country	Mali
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Buea
Country	Cameroon
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Colombo
Department	Department of Parasitology
Country	Sri Lanka
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Malawi
Country	Malawi
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Maryland
Department	Centre for Vaccine Development (CVD)
Country	United States
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Michigan
Country	United States
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	University of Oxford
Department	Oxford University Clinical Research Unit Vietnam (OUCRU)
Country	Viet Nam
Sector	Academic/University
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Malaria Genomic Epidemiology Network (MalariaGEN)
Organisation	Wellcome Trust
Department	KEMRI-Wellcome Trust Research Programme
Country	Kenya
Sector	Multiple
PI Contribution	I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics.
Collaborator Contribution	MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access.
Impact	See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.


Description	Plasmodium Diversity Network Africa
Organisation	Addis Ababa University
Department	Aklilu Lemma Institute of Pathobiology
Country	Ethiopia
Sector	Academic/University
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Congo National Institute of Biomedical Research
Country	Congo, the Democratic Republic of the
Sector	Public
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Cote D'Ivoire's National Institute of Public Health
Department	Malaria Research and Control Centre
Country	Cote d'Ivoire
Sector	Public
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Medical Research Council (MRC)
Department	MRC Unit, The Gambia
Country	Gambia
Sector	Public
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	National Institute for Medical Research, Tanzania
Department	NIMR Mbeya Research Centre
Country	Tanzania, United Republic of
Sector	Public
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Navrongo Health Research Centre (NHRC)
Country	Ghana
Sector	Public
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Noguchi Memorial Institute for Medical Research (NMRR)
Country	Ghana
Sector	Learned Society
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	Pasteur Institute of Madagascar
Country	Madagascar
Sector	Charity/Non Profit
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	University of Bamako
Department	Malaria Research and Training Centre (MRTC) Bamako
Country	Mali
Sector	Academic/University
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	University of Buea
Department	Department of Biochemistry and Microbiology
Country	Cameroon
Sector	Academic/University
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Plasmodium Diversity Network Africa
Organisation	University of Health Sciences, Gabon
Country	Gabon
Sector	Academic/University
PI Contribution	CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship.
Collaborator Contribution	The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists.
Impact	Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative.
Start Year	2013


Description	Tracking Resistance to Artemisinin Collaboration
Organisation	Wellcome Trust
Department	Mahidol University-Oxford Tropical Medicine Research Programme
Country	Thailand
Sector	Academic/University
PI Contribution	The TRAC (Tracking Resistance to Artemisinins Collaboration) study is coordinating prospective clinical and parasitological studies to assess artemisinin susceptibility in 1500 patients in 15 sites across Asia and Africa. This series of studies will provide well characterized malaria parasites with defined parasite clearance profiles for laboratory and molecular characterization, giving us a unique opportunity to identify a molecular marker of artemisinin resistance and validate an accurate laboratory test to detect resistance. The MRC Centre for Genomics and Global Health is supporting TRAC to perform a genome-wide association study of genetic correlates of delayed parasite clearance, based on genome sequencing of parasites in clinical samples. Initial work is focusing on establishing systems to manage the hundreds of terabytes of raw sequence data generated by this project. Also implementing a process of discovering and validating novel SNPs and other forms of genome variation in these samples, primarily based on alignment to the P.falciparum reference genome but also employing new methods of de-novo genome assembly that are currently under development. Having constructed a comprehensive catalogue of both novel and previously-reported variants, we will carry out genotyping of each sample, using statistical methods for quality assurance that have been validated using independent benchmarks. Having determined genotypes for each sample, we will carry out analyses of genetic association with the clinical phenotype. The aim of this project is that the results will be shared with the research community through user-friendly web tools that will allow scientists and public health authorities to navigate the massive quantities of information generated by the TRAC project.
Collaborator Contribution	see above
Impact	This project is at an early stage. We have already released genome sequence data on 1000 P. falciparum samples.
Start Year	2011


Description	UKCRC Modernising Medical Microbiology consortium
Organisation	Oxford University Hospitals NHS Foundation Trust
Country	United Kingdom
Sector	Public
PI Contribution	We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution	See above
Impact	Web application is in development
Start Year	2009


Description	UKCRC Modernising Medical Microbiology consortium
Organisation	Public Health England
Country	United Kingdom
Sector	Public
PI Contribution	We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution	See above
Impact	Web application is in development
Start Year	2009


Description	UKCRC Modernising Medical Microbiology consortium
Organisation	The Wellcome Trust Sanger Institute
Country	United Kingdom
Sector	Charity/Non Profit
PI Contribution	We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution	See above
Impact	Web application is in development
Start Year	2009


Description	UKCRC Modernising Medical Microbiology consortium
Organisation	University of Oxford
Department	Nuffield Department of Clinical Medicine
Country	United Kingdom
Sector	Academic/University
PI Contribution	We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens.
Collaborator Contribution	See above
Impact	Web application is in development
Start Year	2009


Description	Wellcome Trust Sanger Institute
Organisation	The Wellcome Trust Sanger Institute
Country	United Kingdom
Sector	Charity/Non Profit
PI Contribution	As head of the Malaria Programme and the Global Health Strategy Group at the Sanger Institute, I'm engaged in all levels of work - scientific, strategic and operational.
Collaborator Contribution	The Sanger Institute provides infrastructure, resources and expertise in large-scale genome sequencing, genome-wide SNP typing, informatics and functional genomics.
Impact	Examples relevant to this grant: 1. The world's largest repository of DNA samples and clinical data for genetic studies of host-parasite interactions in malaria 2. Publication of the first genome-wide association study of human disease susceptibility in Africa 3. A large multicentre case-control study of severe malaria, representing the largest ongoing genome-wide association study of an infectious disease. In December 2011 we completed genotyping of >1 million SNPs on >20,000 individuals from 10 different populations.
Start Year	2006


Description	WorldWide Antimalarial Resistance Network
Organisation	Menzies School of Health Research
Country	Australia
Sector	Academic/University
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	WorldWide Antimalarial Resistance Network
Organisation	University of Cape Town
Country	South Africa
Sector	Academic/University
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	WorldWide Antimalarial Resistance Network
Organisation	University of Maryland
Country	United States
Sector	Academic/University
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	WorldWide Antimalarial Resistance Network
Organisation	University of Oxford
Department	Nuffield Department of Clinical Medicine
Country	United Kingdom
Sector	Academic/University
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	WorldWide Antimalarial Resistance Network
Organisation	University of Washington
Country	United States
Sector	Academic/University
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	WorldWide Antimalarial Resistance Network
Organisation	World Health Organization (WHO)
Country	Global
Sector	Public
PI Contribution	As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks.
Collaborator Contribution	WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals.
Impact	The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website.
Start Year	2008


Description	Cambodia Manuscript Press Release
Form Of Engagement Activity	A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme?	No
Geographic Reach	International
Primary Audience	Media (as a channel to the public)
Results and Impact	A press release and associated follow up interviews led to media coverage of 64 stories in 13 languages (mostly in English, 78%); National coverage in 23 countries; High-profile coverage included Wired UK, BBC, The Guardian, FoxNews, AFP. Coverage on twitter included 12 tweets from accounts such as BBC World Service, Times of India, and Agence France Presse reached a combined following of 1.3 million users. see above
Year(s) Of Engagement Activity	2013


Description	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	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

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