Consortial Project 3
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.
- Burkina Faso (BF)
- Cameroon (CM)
- Kenya (KE)
- Ghana (GH)
- Papua New Guinea (PG)
- Tanzania (TZ)
- The Gambia (GM)
- Vietnam (VN)
Data
Some data used in this project is available through the 1000 Genomes FTP site and the European Nucleotide Archive.
Current
Whole genome sequencing of six ethnic groups from Burkina Faso, Cameroon, and Tanzania
Whole genome sequence data on 374 individuals from six ethic groups from 3 countries.
Gambian Genome Variation Project - Open Access Data
Low coverage sequencing of the Fula, Jola, Mandinka and Woloff from Gambia Western Division.
People
Investigators involved in Consortial Project 3 include:
Dr Alphaxard Manjurano
Dr Carolyne Ndila
Prof Chris Drakeley
Projects
Partner studies
Prof David Conway
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
Dr Edith Bougouma
Prof Eleanor Riley
Prof Eric Akum Achidi
Prof Gilbert Kokwaro
Projects

Dr Giorgio Sirugo
Hugh Reyburn
Prof Ivo Mueller
Projects
Partner studies
- 1021 Building a national repository of malaria isolates in Papua New Guinea
- 1050 Developing the Plasmodium vivax Genome Variation project with partners in Papua New Guinea
- 1062 Understanding malaria parasite populations and outbreaks in Papua New Guinea
- Human genetic determinants of severe malaria in Papua New Guinea
Dr Julie Makani
Dr Kalifa Abubakr Bojang
Prof Kevin Marsh
Prof Kwadwo Koram
Dr Laurens Manning
MalariaGEN Affiliations
Projects
Partner studies
Dr Lucas Amenga-Etego
MalariaGEN Affiliations
Projects
- Consortial Project 1
- Consortial Project 3
- Genomic Surveillance Hubs in West Africa (NIHR Global Health Research Group)
- P. falciparum Community Project
- Pan-African Malaria Genetic Epidemiology Network (PAMGEN)
- 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
- 1268 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Plasmodium falciparum samples
- 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
Dr Muminatou Jallow
MalariaGEN Affiliations
Projects
Partner studies

Nguyen Thi Ngoc Quyen
MalariaGEN Affiliations
Projects
Partner studies

Dr Norbert Peshu
Assoc Prof Pascal Michon
Dr Sarah Dunstan
Dr Sodiomon Bienvenu Sirima
Dr Tobias Apinjoh
MalariaGEN Affiliations
Projects
- Consortial Project 1
- Consortial Project 3
- P. falciparum Community Project
- Pan-African Malaria Genetic Epidemiology Network (PAMGEN)
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
- 1268 Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Plasmodium falciparum samples
- Human genetic determinants of severe malaria in three regions of Cameroon
Prof Tom Williams
Prof Tran Tinh Hien
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