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)
  • Burkina Faso (BF)
  • Cambodia (KH)
  • Cameroon (CM)
  • Colombia (CO)
  • Congo (Democratic Republic of the Congo) (CD)
  • Ghana (GH)
  • Guinea (GN)
  • Indonesia (ID)
  • Kenya (KE)
  • Laos (LA)
  • Madagascar (MG)
  • Malawi (MW)
  • Mali (ML)
  • Myanmar (MM)
  • Nigeria (NG)
  • Papua New Guinea (PG)
  • Peru (PE)
  • 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

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:

Prof Abdoulaye Djimdé
Associate Professor of Parasitology and Mycology; Chief of the Molecular Epidemiology and Drug Resistance Unit
Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Mali
Wellcome Trust International Fellow
Malaria Programme, Wellcome Trust Sanger Institute, UK
Dr Abraham Oduro
Director
Navrongo Health Research Centre, Ghana
Dr Abraham V O Hodgson
Ghana Health Service, Ministry of Health, Ghana
Prof Alexis Nzila
Associate Professor
King Fahid University of Petroleum and Minerals (KFUMP), Saudi Arabia
Alex Shayo
Nelson Mandela Institute of Science and Technology, Tanzania
Dr Alfred Amambua-Ngwa
Medical Research Council Unit, The Gambia
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
Prof Arjen Dondorp
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, Thailand
Caterina A. Fanello
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, Thailand
Chanaki Amaratunga
NIH National Institute of Allergy and Infectious Diseases (NIAID), 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 Echeverri‐Garcia
Researcher
International Center for Medical Research and Training - CIDEIM, Colombia
Maj Edwin Kamau
Microbiologist
Department of Pathology and Laboratory Services, Walter Reed National Military Medical Center, Bethesda, MD USA
Dr Elizabeth Ashley
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, 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)
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 Trust 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
Dr Marie A. Onyamboko
Kinshasa School of Public Health, University of Kinshasa, DRC
Assoc Prof Mayfong Mayxay
Head of Field Research
Wellcome Trust-Mahosot Hospital Oxford University Medicine Research Collaboration (LOMWRU)
Vice-Dean for Research and Chairman of Research Promotion and Management of UHS
Faculty of Postgraduate Studies, University of Health Sciences (UHS), Vientiane, Laos
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
Prof Nicholas Day
Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford, 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), University of Oxford, 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
NIH National Institute of Allergy and Infectious Diseases (NIAID), 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
NIH National Institute of Allergy and Infectious Diseases (NIAID), 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
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 & Tropical Medicine, UK
Associate Professor
Radboud University Medical Center, The Netherlands
Dr Vandana Thathy
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
NIH National Institute of Allergy and Infectious Diseases (NIAID), USA