P. falciparum Community Project

 

 

 

Started 2010

The P. falciparum Community Project provides researchers with high-quality genotypes linked to a global resource characterising genetic variation in P. falciparum populations.

Objectives & Coordination

The P. falciparum Community Project connects multiple research groups, each acquiring data on parasite genome variation — often in different geographical locations and for different scientific reasons. Working with this community, our long-term goal is to generate accessible information to improve malaria control.

The project is managed by the MalariaGEN Resource Centre. See the P. falciparum Community Project description for more information on the project structure, and data release and publication policies.

Our work is focused on four related objectives:

Building a catalogue of variation and allele frequencies

By aggregating data across many samples, we're able to identify thousands of variations with a high-level of confidence and estimate their frequencies in different groups of samples. We're building a catalogue of variation in the P. falciparum genome based on sequence data analysis, together with estimated allele frequencies in different geographical regions based on aggregated analysis of all the samples and data that have been contributed.

The catalogue is updated periodically — as the number of samples increases, as we incorporate data from different locations, and as sequencing technologies and analytical methods improve.

Providing researchers with standardised genotype data on their samples

Our sequence data analysis pipeline provides researchers with high-quality genotype calls on their samples in a standardised format which enables reliable comparisons to be made with data from other studies and geographical locations.

Publishing global analyses of genome variation, population genetics and evolutionary selection

We'll report on the major geographical divisions of parasite population structure and use this to calculate allele frequency data, as well as analysing other aspects of genome variation, population genetics and evolutionary selection that can best be achieved using the aggregated dataset. These global analyses will be reported through peer-reviewed publications subject to the agreement of the groups who have contributed samples and data. Where appropriate, this will be done through mechanisms such as the Pf3k Project that bring together expert working groups and integrate multiple sources of data to produce specific analytical outputs.

Creating online tools to maximise the reach and impact of project findings

We've developed a set of web tools to enable contributing researchers to explore and analyse sequence read data and genotype calls on their own samples. We have also partnered with the MRC Centre of Genomics and Global Health to build a comprehensive web application to provide the wider research community with user-friendly tools to browse and query project data (www.malariagen.net/apps/pf).

Sampling locations

  • Bangladesh (BD)
  • Benin (BJ)
  • Burkina Faso (BF)
  • Cambodia (KH)
  • Cameroon (CM)
  • Colombia (CO)
  • Congo (Democratic Republic of the Congo) (CD)
  • Ethiopia (ET)
  • Ghana (GH)
  • Guinea (GN)
  • Indonesia (ID)
  • Ivory Coast (CI)
  • Kenya (KE)
  • Laos (LA)
  • Madagascar (MG)
  • Malawi (MW)
  • Mali (ML)
  • Mauritania (MR)
  • Myanmar (MM)
  • Nigeria (NG)
  • Papua New Guinea (PG)
  • Peru (PE)
  • Senegal (SN)
  • Tanzania (TZ)
  • Thailand (TH)
  • The Gambia (GM)
  • Uganda (UG)
  • Vietnam (VN)

Partner studies

We work with a number of researchers undertaking independent studies to address unique questions about malaria biology and disease in malaria endemic areas. Each study is different, but they all involve a genomic component whereby they partner with us to sequence parasite samples and share the population genetic data. Click a link below to learn more about their work.

Data

We routinely release genotype data to our partners. Learn more about data release to partners.

Current

13 Nov 2020

Catalogue of Genetic Variation in P. falciparum - v6.0

Species: P. falciparum

Sample information for 7,113 samples from 29 countries
Genotypes for 5,970 samples from 29 countries

  • ENA Accessions
  • Genotype data
  • Sample metadata
  • SNPs
15 Jan 2016

P. falciparum Community Project Jan. 2016 data release

Species: P. falciparum

Sample information for 3,411 samples from 23 countries
Genotypes for 3,394 samples from 22 countries

19 Aug 2015

Catalogue of Genetic Variation in P. falciparum - v4.0

Species: P. falciparum

Sample set: 3,488 samples from 23 countries

High-quality SNPs: 900,000+

Archive

19 Jan 2015

P. falciparum sample information

Species: P. falciparum

Sample information for P. falciparum samples and sequence data included in previous published population-level analyses

27 Feb 2014

Catalogue of Genetic Variation in P. falciparum - v3.1

Species: P. falciparum

Sample set: 3,251 samples from 20 countries

High-quality SNPs: 681,587

26 Sep 2013

Catalogue of Genetic Variation in P. falciparum - v2.2

Species: P. falciparum

Sample set: 2,155 samples from 19 countries

High-quality SNPs: 531,916

22 May 2012

Catalogue of Genetic Variation in P. falciparum - v1.0

Species: P. falciparum

Sample set: 227 samples from 6 countries

High-quality SNPs: 86,000

People

Investigators involved in the P. falciparum Community Project include:

Dr Abraham Hodgson

Ghana Health Service, Ministry of Health, Ghana

Alex Shayo

Nelson Mandela Institute of Science and Technology, Tanzania

Prof Alexis Nzila

Associate Professor
King Fahid University of Petroleum and Minerals (KFUMP), Saudi Arabia

Prof Alister Craig

Professor of Molecular Parasitology and Dean of Biological Sciences
Liverpool School of Tropical Medicine, UK
Malawi-Liverpool-Wellcome Trust Clinical Research Programme

Chanaki Amaratunga

National Institute of Allergy and Infectious Diseases (NIAID), NIH , USA

Prof Chris Newbold

Weatherall Institute of Molecular Medicine, University of Oxford, UK

Dr Christiane Dolecek

Nuffield Department of Medicine, University of Oxford, UK

Dr Deus Ishengoma

Researcher
National Institute for Medical Research (NIMR), United Republic of Tanzania
Researcher
East African Consortium for Clinical Research (EACCR), United Republic of Tanzania

Dr Diego F Echeverry

Researcher
Centro Internacional de Entrenamiento e Investigaciones Médicas - CIDEIM, Cali, Colombia
Universidad Icesi, Cali, Colombia

Maj Edwin Kamau

Microbiologist
Walter Reed Army Institute of Research, U.S. Military HIV Research Program, Silver Spring, MD, USA

Dr Elizabeth Ashley

Mahidol Oxford Tropical Medicine Research Unit (MORU), Thailand

Dr G L Abby Harrison

Postdoctoral Scientist
Walter and Eliza Hall Institute, Australia

Dr Gordon Awandare

Senior Lecturer, Head, Department of Biochemistry Cell and Molecular Biology
University of Ghana, Legon, Ghana
Director
West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Ghana

Dr Harold Ocholla

Investigator
Malaria Capacity Development Consortium
KEMRI - Centres for Disease Control and Prevention (CDC) Research Program, Kisumu, Kenya
Centre for Bioinformatics and Biotechnology, University of Nairobi, Kenya

Dr Jean-Bosco Ouedraogo

Institut de Recherche en Sciences de la Santé, Burkina Faso

Dr Julian C Rayner

Senior Group Leader, Malaria Programme
Wellcome Sanger Institute, UK
Director, Courses, Conferences and Public Engagement Programme
Wellcome Genome Campus, UK

Dr Lastenia Ruiz

Universidad Nacional de la Amazonia Peruana, Peru

Livingstone Tavul

Papua New Guinea Institute of Medical Research, PNG

Prof Maciej Boni

Head of Mathematical Modelling Group
Oxford University Clinical Research Unit (OUCRU), Vietnam
Associate Professor
Nuffield Department of Medicine, University of Oxford, UK

Assoc Prof Mayfong Mayxay

Head of Field Research
Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Vientiane, Lao PDR
Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR

Dr Milijaona Randrianarivelojosia

Head of Malaria Research Unit
Institut Pasteur de Madagascar
Part-time lecturer
Universités d'Antananarivo et de Mahajanga, Madagascar

Dr Myat Phone Kyaw

The Myanmar Oxford Clinical Research Unit, University of Oxford, Myanmar
University of Public Health, Yangon, Myanmar

Prof Nicholas Day

Mahidol Oxford Tropical Medicine Research Unit (MORU), Thailand

Prof Nicholas J White

Professor of Tropical Medicine and Chair of Wellcome Trust SE Asian Tropical Medicine Research Programmes
Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand

Dr Oralee Branch

NYU School of Medicine Langone Medical Center, USA

Dr Oumou Maïga-Ascofaré

Research Fellow
Bernhard Nocht Institute for Tropical Medicine, Germany
Research Fellow
Research in Tropical Medicine, Kwame Nkrumah University of Sciences and Technology, Kumasi, Ghana
Associate Scientist
Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Mali

Dr Patrick Duffy

National Institute of Allergy and Infectious Diseases (NIAID), NIH, USA

Prof Peter Siba

Papua New Guinea Institute of Medical Research, PNG

Dr Peter C Bull

Group Leader
Department of Pathology, University of Cambridge, UK
KEMRI Wellcome Trust Research Programme, Kenya

Dr Pharath Lim

National Institute of Allergy and Infectious Diseases (NIAID), NIH, USA
Medical Care Development International, Maryland, USA

Prof Ric N Price

Professor of Tropical Medicine
Centre for Tropical Medicine and Global Health, University of Oxford, UK
Professor of Global Health
Menzies School of Health Research, Darwin, Australia
Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand

Dr Rick Fairhurst

Chief, Malaria Pathogenesis and Human Immunity Unit
National Institutes of Health (NIH), USA

Dr Shannon Takala-Harrison

Center for Vaccine Development and Global Health, University of Maryland, School of Medicine, Baltimore, MD, USA

Souleymane Dama

Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Mali

Prof Steffen Borrmann

Institute for Tropical Medicine, University of Tübingen, Germany

Dr Teun Bousema

Senior Lecturer
London School of Hygiene and Tropical Medicine, UK
Associate Professor
Radboud University Medical Center, The Netherlands

Dr Vandana Thathy

Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York, USA
KEMRI Wellcome Trust Research Programme, Kenya

Vito Baraka

Research Scientist
National Institute for Medical Research (NIMR), United Republic of Tanzania
PhD fellow
Department of Epidemiology, International Health Unit, Universiteit Antwerpen, Belgium

Prof William Yavo

Head of the Malaria Research and Control Center
Malaria Research and Control Center of the National Institute of Public Health, Côte d’Ivoire
Professor of Parasitology and Mycology
University Félix Houphouët Boigny, Côte d’Ivoire

Dr Xin-zhuan Su

Chief, Malaria Functional Genomics Section, LMVR
National Institute of Allergy and Infectious Diseases (NIAID), NIH, USA