MalariaGEN - Malaria Genome Epidemiology Network

Background

Malaria is a disease that afflicts hundreds of millions of people and kills about a million children each year. As well as causing much human suffering, malaria is a massive socioeconomic burden for many of the poorest countries in the world. The disease is caused by Plasmodium parasites that invade human red blood cells. The parasites are transmitted from person to person by blood-sucking Anopheles mosquitoes.

One of the main obstacles to controlling malaria is an evolutionary 'arms race' that is going on between parasites, mosquitoes and humans. Parasites and mosquitoes are continually acquiring genetic changes to overcome human efforts to the control the disease with anti-malarial drugs, insecticides and other public health interventions. The other side of the coin is that human populations exposed to malaria have also acquired genetic changes that help to protect against malaria - but some of these are a mixed blessing as they can lead to other disorders such as sickle cell disease.

Aims of the Partnership

A global network for the genomic epidemiology of malaria

MalariaGEN is the Malaria Genomic Epidemiology Network. We are a community of researchers in more than 20 countries who are working together to understand how genome variation in human, Plasmodium and Anopheles populations affects the biology and epidemiology of malaria, and to use this knowledge to develop improved tools for controlling malaria.

Our goals are:

• To expedite the development of an effective vaccine by discovering human genetic variants that determine natural resistance to malaria, and by discovering Plasmodium genetic mechanisms that enable parasites to evade the human immune system.
• To develop new approaches for monitoring anti-malarial drug resistance and preventing it spreading, by analysis of Plasmodium genome variation, population structure and recent evolutionary selection.
• To support innovative strategies for vector control by analysis of Anopheles genome variation, population structure, gene flow, insecticide resistance and anti-parasitic host defence.

To address these problems we've established policies for data-sharing that allow large-scale collaborative projects to be conducted across multiple populations, bringing together detailed clinical and epidemiological data with state-of-the-art technologies for genome sequencing and web tools for data analysis. The work of the network is coordinated by a resource centre whose members are based at Oxford University, the Wellcome Trust Sanger Institute, the London School of Hygiene and Tropical Medicine, and the Wellcome-Mahidol Unit in Bangkok.

Funding

MalariaGEN brings together partner studies around the world that are funded from a range of sources. The MalariaGEN resource centre, which provides stewardship of the central resource of samples and data, together with support for sequencing, genotyping, informatics, ethics and capacity building, is funded primarily by the Wellcome Trust.

The foundations for a data-sharing network in the genomic epidemiology of malaria were developed in 2003-5 with grants from the Medical Research Council and the Gates Foundation. MalariaGEN was formally established in 2005 as part of the Grand Challenges in Global Health initiative, with joint funding from the Wellcome Trust and the Gates Foundation through the Foundation for the National Institutes of Health.

Other substantial contributions to MalariaGEN's core activities come from the Wellcome Trust Sanger Institute and the MRC Centre for Genomics and Global Health. MalariaGEN is part of the European Union EviMalar network.

Partners

MalariaGEN is a continuously growing community of researchers in over 20 countries. Below is a list of several, but not all of the MalariaGEN partners, for more information on our partners please see our website.

• Burkina Faso: Centre National de Recherche et de Formation sur le Paludisme (CNRFP)
• Cameroon: University of Buea
• France: Institut Pasteur
• Gambia: MRC Laboratories
• Germany: Bernhard Nocht Institute for Tropical Medicine (BNI)
• Ghana: Navrongo Health Research Centre
• Ghana: Kwame Nkrumah University of Science and Technology
• Ghana: Noguchi Memorial Institute for Medical Research
• Italy: University of Rome 'La Sapienza'
• Kenya: KEMRI-Wellcome Research Programme
• Malawi: Blantyre Malaria Project
• Malawi: Malawi-Liverpool Wellcome Clinical Research Programme
• Mali: Malaria Research and Training Centre, University of Bamako
• Nigeria: Institute of Child Health, College of Medicine, University of Ibadan
• Papua New Guinea: Papua New Guinea Institute of Medical Research
• Senegal: Institut Pasteur de Dakar
• Sri Lanka: Faculty of Medicine, University of Colombo
• Sudan: Institute for Endemic Diseases, University of Khartoum
• Sweden: Wenner-Gren Institute, University of Stockholm
• Tanzania: Muhimbili University of Health and Allied Sciences
• Tanzania: National Institute for Medical Research
• Tanzania: Genome Science Center, Sokoine University
• Tanzania: Joint Malaria Programme, Kilimanjaro Christian Medical Centre
• Thailand: Faculty of Medicine Siriraj Hospital, Mahidol University
• Thailand: Faculty of Tropical Medicine, Mahidol University
• UK: Swansea University
• UK: Wellcome Trust Centre for Human Genetics, University of Oxford
• UK: Ethox Centre, Department of Public Health, University of Oxford
• UK: London School of Hygiene & Tropical Medicine
• UK: National Institute for Biological Standards and Control
• UK: Wellcome Trust Sanger Institute
• USA: University of Maryland
• USA: Michigan State University
• USA: Seattle Biomedical Research Institute
• Vietnam: Oxford University Clinical Research Unit

Publications

• Methodological challenges of genome-wide association analysis in Africa.

  Teo YY, Small KS and Kwiatkowski DP

  Nature reviews. Genetics 2010;11;2;149-60

  PUBMED: 20084087; DOI: 10.1038/nrg2731

• Ethical data release in genome-wide association studies in developing countries.

  Parker M, Bull SJ, de Vries J, Agbenyega T, Doumbo OK and Kwiatkowski DP

  PLoS medicine 2009;6;11;e1000143

  PUBMED: 19956792; PMC: 2771895; DOI: 10.1371/journal.pmed.1000143

• Genome-wide and fine-resolution association analysis of malaria in West Africa.

  Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, SanJoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP, Wellcome Trust Case Control Consortium and Malaria Genomic Epidemiology Network

  Nature genetics 2009;41;6;657-65

  PUBMED: 19465909; PMC: 2889040; DOI: 10.1038/ng.388

• A global network for investigating the genomic epidemiology of malaria.

  Malaria Genomic Epidemiology Network

  Nature 2008;456;7223;732-7

  PUBMED: 19079050; DOI: 10.1038/nature07632

• Valid consent for genomic epidemiology in developing countries.

  Chokshi DA, Thera MA, Parker M, Diakite M, Makani J, Kwiatkowski DP and Doumbo OK

  PLoS medicine 2007;4;4;e95

  PUBMED: 17455985; PMC: 1876398; DOI: 10.1371/journal.pmed.0040095

• Standardized data collection for multi-center clinical studies of severe malaria in African children: establishing the SMAC network.

  Taylor T, Olola C, Valim C, Agbenyega T, Kremsner P, Krishna S, Kwiatkowski D, Newton C, Missinou M, Pinder M and Wypij D

  Transactions of the Royal Society of Tropical Medicine and Hygiene 2006;100;7;615-22

  PUBMED: 16551469; PMC: 1459261; DOI: 10.1016/j.trstmh.2005.09.021

Ethics & governance

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.

To download our publications and policies on best practice for recruitment of research participants, data management and data sharing and for more information on our governance structure please see our website.