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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.


Samples were collected from 2,217 individuals through a number of community-based studies.

Sampling locations

Burkina Faso, Cameroon, The Gambia, Ghana, Kenya, Papua New Guinea, Tanzania, Vietnam.


Some data used in this project is available through the 1000 Genomes FTP site and the European Nucleotide Archive.


15 Aug 2019 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.

This data is subject to
Human GWAS data

19 Jul 2019 Gambian Genome Variation Project - Open Access Data

Low coverage sequencing of the Fula, Jola, Mandinka and Woloff from Gambia Western Division.

Open Access
Open access