Pf3k Consortium releases data on more than 2,500 P. falciparum genomes
The Pf3k Consortium has made its third public data release, the first to include data on all samples in the pilot phase of the project. Consisting of sample information, analysis BAMs and preliminary baseline genotypes for 2,512 samples collected from major malaria-endemic regions in Africa and Asia, this represents one of the largest collections of open access Plasmodium falciparum genomes in the world.
This release comes at a time when the latest wave of antimalarial drug resistance, including the frontline drug, artemisinin, is threatening gains made against malaria.
“The parasites that cause malaria have a tremendous capacity to adapt to our attempts to control them,” warns Dominic Kwiatkowski of the University of Oxford and the Wellcome Trust Sanger Institute. “Drug resistance is the result of a complex evolutionary process, and we need to build resources that will ultimately allow malaria control programmes to monitor and respond to these changes in near real-time.”
This was the impetus for a new global collaboration, the Pf3k Consortium, which was established less than a year ago with the aim of analysing 3,000 P. falciparum samples from the major malaria-endemic regions of the world in order to generate a high-resolution view of natural variation in the parasite.
The pilot phase of the Pf3k project is focused on overcoming many of the technical challenges associated with analysing such a complex genome, by providing solid reference genomes, good baseline data and reliable analytical methods. One example of this work is the development of reference genomes drawn from different populations, which will help researchers to accurately identify genetic changes in parasites sampled directly from patients in different parts of the world.
Reflecting a commitment to the early release of data, the Pf3k Consortium have made their pilot data available under the Fort Lauderdale conditions, and the data can be downloaded or explored using a dedicated web application.
The Pf3k data can be explored online using the Panoptes software platform developed by the MRC’s Centre for Genomics and Global Health (CGGH). This platform has been developed to allowed clinicians and scientists around the world to analyse and share data generated through large-scale collaborations such as Pf3k.
“Panoptes is proving to be a powerful tool for researchers working with genomic data,” explains Dr Ben Jeffery, one of the developers working at CGGH. “With the Pf3k web application, we're just getting started with features such as the searchable genome browser which allows you to explore and download the data—making it as accessible as possible. As the Pf3k project evolves, there will be the option to include even more data, for example allele frequencies and neighbour-joining trees, as we've done in the Panoptes-based Ag1000G application."
The Pf3k project is led by researchers at the Broad Institute, the University of Oxford and the Wellcome Trust Sanger Institute.
Learn more about the Pf3k Consortium: www.malariagen.net/projects/parasite/pf3k
Explore the data: www.malariagen.net/apps/pf3k
Read more about the Pf3k project's pilot phase: https://sangerinstitute.wordpress.com/2015/04/24/keeping-pace-with-changing-parasite-genetics/