Consortial Project 3
Started 2005
Consortial Project 3 used whole genome sequencing to identify genetic diversity in genes known to be associated with resistance to severe malaria, within and across malaria-endemic populations.
Objectives & Coordination
Human genome diversity in malaria-endemic regions
Our primary objective was to characterise genetic diversity in genes known to be associated with malaria.
This work has involved:
- Establishing a framework for sample collection and data-sharing for genotyping and whole genome sequencing
- Capillary sequencing on exonic regions of the HBA, HBB, G6PD, and SLC4A1 gene regions in eight of the populations sampled
- Preparing all the CP3 samples for whole genome amplification
- Working to define a reliable methodology for multi-centre genome-wide association studies (GWAS) in Africa
This project began shortly after MalariaGEN was formed in 2005, and has greatly influenced our approach to collaborative science.
Sampling locations
Samples were collected from 2,217 individuals through a number of community-based studies.
Data
Some data used in this project is available through the 1000 Genomes FTP site and the European Nucleotide Archive.
People
Investigators involved in Consortial Project 3 include:
Dr Alphaxard Manjurano
London School of Hygiene & Tropical Medicine, UK
Dr Carolyne Ndila
KEMRI Wellcome Trust Research Programme, Kenya
Prof Chris Drakeley
Professor
London School of Hygiene and Tropical Medicine, UK
Projects
Partner studies
Prof David Conway
London School of Hygiene and Tropical Medicine, UK
Projects
Partner studies
- 1006 Genome-wide analysis of genetic variation in The Gambia
- 1026 Effects of transmission intensity on population structure and signatures of selection in Guinea
- 1083 Alternative molecular mechanisms for erythrocyte invasion by Plasmodium falciparum in Ghana
- 1134 Population genetics of Plasmodium falciparum in West Africa
- 1135 Parasite adaption in Senegal at molecular, functional and population level
- 1147 Population genetics of Plasmodium falciparum parasites in Mauritania
- 1183 Alternative mechanisms for erythrocyte invasion by Plasmodium falciparum
- Human genetic determinants of severe malaria in The Gambia
Prof David Modiano
Sapienza University of Rome, Italy
Dr Edith Bougouma
Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Burkina Faso
Prof Eleanor Riley
London School of Hygiene & Tropical Medicine, UK
Prof Eric Akum Achidi
University of Buea, Cameroon
Prof Gilbert Kokwaro
University of Nairobi, Kenya
Projects
Dr Giorgio Sirugo
Head, Genetics Center
Ospedale San Pietro Fatebenefratelli, Rome, Italy
Hugh Reyburn
London School of Hygiene & Tropical Medicine, UK
Prof Ivo Mueller
Walter and Eliza Hall Institute, Parkville, Victoria, Australia
University of Melbourne, Australia
Dr Julie Makani
Senior Lecturer
Muhimbili University of Health and Allied Sciences, Tanzania
Research Fellow in Tropical Medicine
University of Oxford, UK
Intermediate Fellow
Wellcome Trust, UK
Dr Kalifa Abubakr Bojang
Medical Research Council Unit, The Gambia
Prof Kevin Marsh
Professor of Tropical Medicine
Nuffield Department of Medicine, University of Oxford, UK
KEMRI Wellcome Trust Research Programme, Kenya
Prof Kwadwo Koram
University of Ghana, Legon, Ghana
Dr Laurens Manning
Associate Professor
University of Western Australia
Infectious Diseases Physician
Department of Infectious Diseases, Fiona Stanley Hospital
MalariaGEN Affiliations
Projects
Partner studies
Dr Lucas Amenga-Etego
West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
MalariaGEN Affiliations
Projects
- Consortial Project 1
- Consortial Project 3
- Genomic Surveillance Hubs in West Africa (NIHR Global Health Research Group)
- P. falciparum Community Project
- Pf3k
Partner studies
- 1017 Population genetics of natural populations in Northern Ghana
- 1094 Population genetics of Plasmodium falciparum parasites in Northern Ghana
- 1151 Testing the effectiveness of selective whole genome amplification on samples collected in Northern Ghana
- 1168 Genomic surveillance of Plasmodium falciparum in the Kassena-Nankana Districts, Ghana
- 1183 Alternative mechanisms for erythrocyte invasion by Plasmodium falciparum
- 1294 Investigation of Host and Parasite Genetic Factors Mediating asymptomatic Plasmodium falciparum infections
- Human genetic determinants of severe malaria in the Kassena-Nankana District of Northern Ghana
Prof Michael Wilson
Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana
Dr Muminatou Jallow
MRC Laboratories, The Gambia
MalariaGEN Affiliations
Projects
Partner studies
Nguyen Thi Ngoc Quyen
Oxford University Clinical Research Unit (OUCRU), Vietnam
MalariaGEN Affiliations
Projects
Partner studies
Dr Norbert Peshu
KEMRI Wellcome Trust Research Programme, Kenya
Assoc Prof Pascal Michon
FMHS Research Coordinator
Faculty of Medicine & Health Sciences, Divine Word University, Madang, PNG
Dr Sarah Dunstan
Senior Research Fellow
The University of Melbourne, Australia
Dr Sodiomon Bienvenu Sirima
Executive Director
Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Burkina Faso
Scientific Team Leader
Groupe de Recherche Action en Sante (GRAS) Burkina Faso
Dr Tobias Apinjoh
Biochemist and Researcher
University of Buea, Cameroon
MalariaGEN Affiliations
Projects
Partner studies
- 1093 Population genetics of Plasmodium falciparum parasites in South-Western Cameroon
- 1165 Prevalence of gene polymorphisms in symptomatic and asymptomatic Plasmodium falciparum infected individuals from the Southwest region of Cameroon
- Human genetic determinants of severe malaria in three regions of Cameroon
Prof Tom Williams
Head of the Department of Epidemiology and Demography
KEMRI Wellcome Trust Research Programme, Kenya
Chair in Haemoglobinopathy Research
Imperial College London, UK
Prof Tran Tinh Hien
Director of Clinical Research (retired)
Oxford University Clinical Research Unit (OUCRU), Vietnam
Professor of Tropical Medicine, Group Head / PI (retired)
Centre for Tropical Medicine and Global Health, University of Oxford, UK
Projects
- Consortial Project 1
- Consortial Project 3
- GenRe-Mekong
- P. falciparum Community Project
- P. vivax Genome Variation
Partner studies
- 1008 Containment of artemisinin tolerant malaria parasites in Southeast Asia (ARCE)
- 1020 Measuring in vitro drug sensitivity in Vietnam
- 1049 Developing the Plasmodium vivax Genome Variation project with partners in Vietnam
- 1157 P. vivax SNP barcode for mapping parasite transmission and spread within and across borders: a vivaxGEN initiative
- 1181 Monitoring the susceptibility of Plasmodium falciparum to antimalarial drugs in malaria endemic areas in southern Vietnam
- Human genetic determinants of severe Plasmodium falciparum malaria in Vietnam
Dr Valentina Mangano
Research Fellow
Sapienza University of Rome, Italy
