article · Wellcome Open Research
The Pf7 data release provides a comprehensive open-access genomic resource detailing variation in the malaria parasite Plasmodium falciparum. Drawing on more than 20,000 samples collected across 33 countries by 82 partner studies, the resource expands geographic coverage to previously underrepresented endemic regions. It incorporates dried blood spot samples processed through selective whole genome amplification, supported by new methods for genotyping copy number variations. The dataset features high-quality calls for six million single nucleotide polymorphisms and short indels. Notable findings include emerging crt gene mutations in parts of Southeast Asia, varied drug resistance profiles across Africa and the Indian subcontinent, and large gene deletions responsible for rapid diagnostic test failures. Additionally, the resource maps sequence variations in the circumsporozoite protein gene relative to the formulations used in the RTS,S and R21 vaccines.
Malaria control relies heavily on effective treatments, accurate diagnostic tests, and emerging vaccines. By mapping genomic diversity across thousands of samples, this open-access resource helps researchers track drug resistance trends and diagnostic failures. These insights support public health bodies and scientists in monitoring parasite evolution and assessing whether current vaccines and therapies remain aligned with circulating strains.
This dataset provides foundational data that can be used immediately by diagnostic manufacturers, vaccine developers, and surveillance programmes. Product developers can evaluate whether diagnostic kits risk failure from specific gene deletions or assess how vaccine target antigens match diverse field strains. As an open-access reference dataset, it serves as an early-stage information resource rather than a direct commercial product.
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<ns3:p> We describe the MalariaGEN Pf7 data resource, the seventh release of <ns3:italic>Plasmodium falciparum</ns3:italic> genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging <ns3:italic>crt</ns3:italic> mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the <ns3:italic>csp</ns3:italic> gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website. </ns3:p>
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DOI: 10.12688/wellcomeopenres.18681.1
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