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.

  • Burkina Faso (BF)
  • Cameroon (CM)
  • Kenya (KE)
  • Ghana (GH)
  • Papua New Guinea (PG)
  • Tanzania (TZ)
  • The Gambia (GM)
  • Vietnam (VN)


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.

19 Jul 2019

Gambian Genome Variation Project - Open Access Data

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


Investigators involved in Consortial Project 3 include:

Dr Edith Bougouma

Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Burkina Faso

Prof Eric Akum Achidi

University of Buea, Cameroon

Prof Gilbert Kokwaro

University of Nairobi, Kenya

Dr Giorgio Sirugo

Head, Genetics Center
Ospedale San Pietro Fatebenefratelli, Rome, Italy

Hugh Reyburn

London School of Hygiene & Tropical Medicine, UK

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

Dr Laurens Manning

Associate Professor
University of Western Australia
Infectious Diseases Physician
Department of Infectious Diseases, Fiona Stanley Hospital

Prof Michael Wilson

Nogouchi Memorial Institute for Medical Research, Legon-Accra, Ghana

Dr Muminatou Jallow

MRC Laboratories, The Gambia

Nguyen Thi Ngoc Quyen

Oxford University Clinical Research Unit (OUCRU), Vietnam

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

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