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
Organisations
- University of Oxford, United Kingdom (Collaboration, Lead Research Organisation)
- University of Colombo, Sri Lanka (Collaboration)
- Public Health England, Salisbury (Collaboration)
- Kwame Nkruma University of Science & Tec (Collaboration)
- University of Cape Town (Collaboration)
- Pasteur Institute Dakar (Collaboration)
- Addis Ababa University, Ethiopia (Collaboration)
- University of Rome I (La Sapienza), Italy (Collaboration)
- Noguchi Memorial Inst for Medical Res (Collaboration)
- University of Malawi, Malawi (Collaboration)
- Papua New Guinea Inst of Med Research (Collaboration)
- Pasteur Institute, Paris (Collaboration)
- Cote D'Ivoire's National Institute of Public Health (Collaboration)
- University of Maryland, United States (Collaboration)
- University of Buea, Cameroon (Collaboration)
- Pasteur Institute of Madagascar (Collaboration)
- Menzies School of Health Research (Collaboration)
- Washington University in St. Louis (Collaboration)
- National Institute for Medical Research (Collaboration)
- Institute for Endemic Diseases IEND (Collaboration)
- The Wellcome Trust Sanger Institute (Collaboration, Fellow)
- London Sch of Hygiene and Trop Medicine, United Kingdom (Collaboration)
- World Health Organization (WHO) (Collaboration)
- Medical Research Council (Collaboration)
- University of Health Sciences, Gabon (Collaboration)
- Mahidol University (Collaboration)
- University of Michigan, United States (Collaboration)
- University of Bamako (Collaboration)
- Congo National Institute of Biomedical Research (Collaboration)
- Wellcome Trust, LONDON (Collaboration)
- Navrongo Health Research Centre (NHRC) (Collaboration)
- University of Stockholm (Collaboration)
- MURAZ Center (Collaboration)
- Liverpool School of Tropical Medicine (Collaboration)
- Oxford University Hospitals NHS Foundation Trust (Collaboration)
People |
ORCID iD |
| Dominic Peter Kwiatkowski (Principal Investigator / Fellow) |
Publications
Almagro-Garcia J
(2009)
SnoopCGH: software for visualizing comparative genomic hybridization data.
in Bioinformatics (Oxford, England)
Amambua-Ngwa A
(2012)
Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.
in PLoS genetics
Atkinson SH
(2008)
Tumor necrosis factor SNP haplotypes are associated with iron deficiency anemia in West African children.
in Blood
Atkinson SH
(2006)
Seasonal childhood anaemia in West Africa is associated with the haptoglobin 2-2 genotype.
in PLoS medicine
Auburn S
(2013)
Effective preparation of Plasmodium vivax field isolates for high-throughput whole genome sequencing.
in PloS one
Auburn S
(2012)
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
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
Band G
(2013)
Imputation-based meta-analysis of severe malaria in three African populations.
in PLoS genetics
| 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 | 08/2005 |
| 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 | 08/2005 |
| End | 06/2010 |
| Description | MRC Programme Grant |
| Amount | £1,500,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2006 |
| 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 | 08/2011 |
| 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 | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Papua New Guinea Institute of Medical Research |
| Country | Papua New Guinea |
| Sector | Public |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Pasteur Institute Dakar |
| Country | Senegal |
| Sector | Charity/Non Profit |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Pasteur Institute, Paris |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Sapienza University of Rome |
| Department | Parasitology Sapienza |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Stockholm University |
| Country | Sweden |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Bamako |
| Department | Malaria Research and Training Centre (MRTC) Bamako |
| Country | Mali |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Buea |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Colombo |
| Department | Department of Parasitology |
| Country | Sri Lanka |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Malawi |
| Country | Malawi |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Maryland |
| Department | Centre for Vaccine Development (CVD) |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Michigan |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | University of Oxford |
| Department | Oxford University Clinical Research Unit Vietnam (OUCRU) |
| Country | Viet Nam |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Malaria Genomic Epidemiology Network (MalariaGEN) |
| Organisation | Wellcome Trust |
| Department | KEMRI-Wellcome Trust Research Programme |
| Country | Kenya |
| Sector | Academic/University |
| PI Contribution | I direct the MalariaGEN Resource Centre (http://www.malariagen.net/). CGGH supports Resource Centre activities, particularly statistics, software engineering, and ethics. |
| Collaborator Contribution | MalariaGEN - the Malaria Genomic Epidemiology Network - is a community of more than 100 researchers in 30 countries, working together on projects that require sharing and integration of large amounts of data. MalariaGEN brings together the work of many different partner studies, each of which is led by an independent investigator and has its own scientific objectives. MalariaGEN adds value to partner studies by providing access to genotyping and sequencing technologies, and by providing a framework for sharing and integrating data in consortial and community projects. MalariaGEN provides training and support in genetic data analysis for researchers at partner institutions in malaria-endemic countries. We do this through a data bursary scheme and through an active programme of scientific meetings and training workshops. These activities are supported by the MalariaGEN Resource Centre which has a team of experts in statistics, population genetics and bioinformatics at the Sanger Institute, Oxford University, the London School of Hygiene and Tropical Medicine, and Mahidol University in Bangkok. There are many practical and ethical challenges involved in sharing data across a global network comprising investigators and institutions with great disparities in funding and infrastructure. The MalariaGEN community has been working to develop transparent procedures for ethics and governance. We have a governance committee and an independent data access committee, and network policies have been defined for data sharing and data access. |
| Impact | See www.malariagen.net for data resources and web applications produced by the network. Major recent outputs include: Anopheles gambiae 1000 Genomes Consortium. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017. 552:96-100. doi: 10.1038/nature24995. PMID:29186111 (Miles and Kwiatkowski are corresponding authors). This is the largest data resource on mosquito genome variation and population genetics. It identifies over 50 million SNPs, with evidence of ancient population expansions and recent bottlenecks, and strong selective sweeps of insecticide-resistance spreading over large geographical distances and between species. All the data were released open access as soon as available (www.malariagen.net/apps/ag1000g ) Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP; Malaria Genomic Epidemiology Network. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017. 356(6343). pii: eaam6393. doi: 10.1126/science.aam6393. PMID: 28522690. By combining GWAS data with genome sequence data from diverse African populations, we discovered a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which reduces the risk of severe malaria by 40%. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Addis Ababa University |
| Department | Aklilu Lemma Institute of Pathobiology |
| Country | Ethiopia |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Congo National Institute of Biomedical Research |
| Country | Congo, the Democratic Republic of the |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Cote D'Ivoire's National Institute of Public Health |
| Department | Malaria Research and Control Centre |
| Country | Cote d'Ivoire |
| Sector | Public |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Medical Research Council (MRC) |
| Department | MRC Unit, The Gambia |
| Country | Gambia |
| Sector | Public |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | National Institute for Medical Research, Tanzania |
| Department | NIMR Mbeya Research Centre |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Navrongo Health Research Centre (NHRC) |
| Country | Ghana |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Noguchi Memorial Institute for Medical Research (NMRR) |
| Country | Ghana |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | Pasteur Institute of Madagascar |
| Country | Madagascar |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | University of Bamako |
| Department | Malaria Research and Training Centre (MRTC) Bamako |
| Country | Mali |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | University of Buea |
| Department | Department of Biochemistry and Microbiology |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Plasmodium Diversity Network Africa |
| Organisation | University of Health Sciences, Gabon |
| Country | Gabon |
| Sector | Academic/University |
| PI Contribution | CGGH has provided small starter grants to PDNA, in part by MRC Centenary Award, as part of our mission to support the training and capacity development of early career African scientists. CGGH continues to support PDNA is various ways including supporting training and providing mentor ship. |
| Collaborator Contribution | The Plasmodium Diversity Network Africa (PDNA) is a partnership of African scientists working together to determine the diversity of the malaria parasite in sub-Saharan Africa and by using this data, inform malaria control policy. PDNA members are leading research programmes in their own contexts and are part of the training and capacity development of early career African scientists. |
| Impact | Since established there are two PDNA led publications and £5m grant funding through the Wellcome Trust Developing Excellence in Leadership, Training and Science Initiative. |
| Start Year | 2013 |
| Description | Tracking Resistance to Artemisinin Collaboration |
| Organisation | Wellcome Trust |
| Department | Mahidol University-Oxford Tropical Medicine Research Programme |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The TRAC (Tracking Resistance to Artemisinins Collaboration) study is coordinating prospective clinical and parasitological studies to assess artemisinin susceptibility in 1500 patients in 15 sites across Asia and Africa. This series of studies will provide well characterized malaria parasites with defined parasite clearance profiles for laboratory and molecular characterization, giving us a unique opportunity to identify a molecular marker of artemisinin resistance and validate an accurate laboratory test to detect resistance. The MRC Centre for Genomics and Global Health is supporting TRAC to perform a genome-wide association study of genetic correlates of delayed parasite clearance, based on genome sequencing of parasites in clinical samples. Initial work is focusing on establishing systems to manage the hundreds of terabytes of raw sequence data generated by this project. Also implementing a process of discovering and validating novel SNPs and other forms of genome variation in these samples, primarily based on alignment to the P.falciparum reference genome but also employing new methods of de-novo genome assembly that are currently under development. Having constructed a comprehensive catalogue of both novel and previously-reported variants, we will carry out genotyping of each sample, using statistical methods for quality assurance that have been validated using independent benchmarks. Having determined genotypes for each sample, we will carry out analyses of genetic association with the clinical phenotype. The aim of this project is that the results will be shared with the research community through user-friendly web tools that will allow scientists and public health authorities to navigate the massive quantities of information generated by the TRAC project. |
| Collaborator Contribution | see above |
| Impact | This project is at an early stage. We have already released genome sequence data on 1000 P. falciparum samples. |
| Start Year | 2011 |
| Description | UKCRC Modernising Medical Microbiology consortium |
| Organisation | Oxford University Hospitals NHS Foundation Trust |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens. |
| Collaborator Contribution | See above |
| Impact | Web application is in development |
| Start Year | 2009 |
| Description | UKCRC Modernising Medical Microbiology consortium |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens. |
| Collaborator Contribution | See above |
| Impact | Web application is in development |
| Start Year | 2009 |
| Description | UKCRC Modernising Medical Microbiology consortium |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens. |
| Collaborator Contribution | See above |
| Impact | Web application is in development |
| Start Year | 2009 |
| Description | UKCRC Modernising Medical Microbiology consortium |
| Organisation | University of Oxford |
| Department | Nuffield Department of Clinical Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have contributed to the development of web informatics tools for the Modernising Medical Microbiology Consortium. This follows on from work funded by this MRC grant to develop the MapSeq web application for population-level analysis of genome variation in parasites and pathogens. |
| Collaborator Contribution | See above |
| Impact | Web application is in development |
| Start Year | 2009 |
| Description | Wellcome Trust Sanger Institute |
| Organisation | The Wellcome Trust Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | As head of the Malaria Programme and the Global Health Strategy Group at the Sanger Institute, I'm engaged in all levels of work - scientific, strategic and operational. |
| Collaborator Contribution | The Sanger Institute provides infrastructure, resources and expertise in large-scale genome sequencing, genome-wide SNP typing, informatics and functional genomics. |
| Impact | Examples relevant to this grant: 1. The world's largest repository of DNA samples and clinical data for genetic studies of host-parasite interactions in malaria 2. Publication of the first genome-wide association study of human disease susceptibility in Africa 3. A large multicentre case-control study of severe malaria, representing the largest ongoing genome-wide association study of an infectious disease. In December 2011 we completed genotyping of >1 million SNPs on >20,000 individuals from 10 different populations. |
| Start Year | 2006 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | Menzies School of Health Research |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | University of Cape Town |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | University of Maryland |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | University of Oxford |
| Department | Nuffield Department of Clinical Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | University of Washington |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | WorldWide Antimalarial Resistance Network |
| Organisation | World Health Organization (WHO) |
| Country | Global |
| Sector | Public |
| PI Contribution | As the Head of Informatics, I provide leadership to the team developing the open-source, web-based informatics tools that underpin WWARN's data sharing and analysis, as well as providing data visualisations that make core findings available open access. This builds on work funded by a previous MRC grant that contributed to the Topheno web application for integration of clinical and epidemiological data across global research networks. |
| Collaborator Contribution | WWARN provides high-quality data resources, customised research tools and services, and a global platform for exchanging scientific and public health information on malaria drug resistance. Since its formation WWARN has grown into a multidisciplinary, global data sharing network with more than 150 collaborators, bringing together researchers, clinicians, and public health professionals. |
| Impact | The following points outline some of the key outputs that have resulted. Developed and deployed a data submission system that accepts clinical, molecular, pharmacological and in vitro data in any format. Designed and built a a sophisticated data repository that stores and connects the different types of data. Built an interactive tool, WWARN Explorer to visualise data relating to antimalarial resistance. Designed and developed the Molecular Surveyor, an interactive map summarising the location and incidence of molecular markers of sulphadoxine pyrimethamine resistance in Plasmodium falciparum dhfr and dhps genes compiled from peer-reviewed publications. Designed and developed the Antimalarial Quality (AQ) Surveyor, a data visualisation tool that tabulates and maps reports of antimalarial quality with summary data for individual surveys. Led the initial design and hosting for the WWARN website. |
| Start Year | 2008 |
| Description | Cambodia Manuscript Press Release |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A press release and associated follow up interviews led to media coverage of 64 stories in 13 languages (mostly in English, 78%); National coverage in 23 countries; High-profile coverage included Wired UK, BBC, The Guardian, FoxNews, AFP. Coverage on twitter included 12 tweets from accounts such as BBC World Service, Times of India, and Agence France Presse reached a combined following of 1.3 million users. see above |
| Year(s) Of Engagement Activity | 2013 |
| Description | 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 |