Plasmodium falciparum population genomics
The partner studies that make up this community project are concerned with a broad range of scientific questions. They include investigations of how malaria parasites invade human red blood cells, how parasites develop resistance against anti-malarial drugs, and why some strains of parasite appear to be more virulent than others. MalariaGEN provides a central resource for high-throughput sequencing and informatics, that enables our research partners to investigate such questions at the level of the whole genome.
In the process of supporting partner studies, we are building a catalog of P. falciparum genome variation as a scientific resource for the malaria research community as a whole. The first version of the catalog (see Data below) contains data on single nucleotide polymorphisms (SNPs) found in 227 parasite samples collected at six different locations in Africa, Asia and Oceania.
The catalog will grow over time as the number of samples increases, as we incorporate data from different locations, and as sequencing technologies and analytical methods improve. We are currently working to increase the number of SNPs that we can genotype with confidence in field samples, and to optimise methods for genotyping other types of polymorphism such as insertions, deletions and copy number variations.
To ensure that this community project meets the needs of the community, MalariaGEN circulated a draft consultation document defining the project in detail, including project aims, and proposed terms for data-sharing, scholarly publication and attribution.
- MalariaGEN consultation document - Community project on Plasmodium falciparum population genomics (version 1, 6 June 2012)
We are grateful to those who responded, providing valuable feedback that is shaping our thinking as we move ahead. We are currently revising the project documentation. Once completed, this information will be made available here.
To help get this community project off the ground, the Wellcome Trust Sanger Centre's Malaria Programme is offering to collaborate with partners on sequencing and analysis of parasite DNA samples. The document below describes the relationship between the Sanger Malaria Programme and this MalariaGEN community project, as well as the procedure for requesting sequencing of parasite DNA samples, and is intended to be a companion to the consultation document above:
Open access data resources:
- Catalog of genetic variations (SNPs) and allele frequencies, release 1.0 - search and query a catalog of SNPs found in P. falciparum field isolates and compare their allele frequencies between populations from different regions of the world
- Sequence read data - open access sequence read data hosted by the European Nucleotide Archive
Managed access data resource:
Data resources for MalariaGEN partners:
- My Genotypes - browse genotype calls for individual parasite samples you have contributed to the community project
- My Studies - view the current status of your contributed samples and download data reports
- Burkina Faso: Genome variation & signatures of Plasmodium falciparum population structure: Jean-Bosco Ouedraogo and colleagues. Study>>
- Cambodia: Genomics of parasite clearance: Rick Fairhurst and colleagues. Study>>
- Cambodia: Studies of artemisinin resistance: Xin zhuan Su, Rick Fairhurst and colleagues. Study>>
- Cambodia, Thailand, Bangladesh: ARC3 study of artemisinin resistance: Chris Plowe and colleagues. Study>>
- Gambia: Genetic variation in Plasmodium falciparum: Alfred Amambua-Ngwa, David Conway and colleagues. Study>>
- Ghana: Malaria epidemiology in Northern Ghana: Abraham Oduro, Lucas Amenga-Etego and colleagues. Study>>
- Kenya: Genome-wide assoctiation study of antimalarial drug resistance: Alexis Nzila, Kevin Marsh, Norbert Peshu, Steffen Borrmann and colleagues. Study>>
- Mali: Signatures of Plasmodium falciparum population structure: Abdoulaye Djimde and colleagues. Study>>
- Papua New Guinea: Plasmodium falciparum genome variation: Ivo Mueller, Peter Siba and colleagues. Study>>
- Tanzania, Mali: Diversity and population structure of malaria parasites: Patrick Duffy and colleagues. Study>>
- Thailand: Drug resistance on the Thai-Burmese border: Tim Anderson and colleagues. Study>>
- UK: Malaria in travellers: Colin Sutherland and colleagues. Study>>
The number of partner studies is constantly growing, so this is not a comprehensive list of the many research groups around the world are contributing samples and expertise to this project.
Manske, Miotto et al. (2012) Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing, Nature