Pf7: An open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
This record provides information about the Pf7 dataset which contains genome variation data on over 20,000 worldwide samples of Plasmodium falciparum. The key publication is MalariaGEN et al, Wellcome Open Research 2023, 8:22 <a title="This opens in a new tab" href="http
This record provides information about the Pf7 dataset which contains genome variation data on over 20,000 worldwide samples of Plasmodium falciparum. The key publication is MalariaGEN et al, Wellcome Open Research 2023, 8:22 https://doi.org/10.12688/wellcomeopenres.18681.1.
Content of the data release
This release contains details on contributing partner studies, sample metadata and key sample attributes inferred from genomic data, and genomic data including raw sequence reads. Further details and analytical results can be found in the accompanying data release paper.
These data are available open access. Publications using these data should acknowledge and cite the source of the data using the following format: “This publication uses MalariaGEN data as described in ‘Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples’ MalariaGEN et al, Wellcome Open Research 2023, 8:22 https://doi.org/10.12688/wellcomeopenres.18681.1.
- Study information: Details of the 82 contributing partner studies, including description, contact information and key people.
- Sample provenance and sequencing metadata: sample information including partner study information, location and year of collection, ENA accession numbers, and QC information for 20,864 samples from 33 countries.
- Measure of complexity of infections: characterisation of within-host diversity (FWS) for 16,203 QC pass samples.
- Drug resistance marker genotypes: genotypes at known markers of drug resistance for 16,203 samples, containing amino acid and copy number genotypes at six loci: crt, dhfr, dhps, mdr1, kelch13, plasmepsin 2-3.
- Inferred resistance status classification: classification of 16,203 QC pass samples into different types of resistance to 10 drugs or combinations of drugs and to RDT detection: chloroquine, pyrimethamine, sulfadoxine, mefloquine, artemisinin, piperaquine, sulfadoxine- pyrimethamine for treatment of uncomplicated malaria, sulfadoxine- pyrimethamine for intermittent preventive treatment in pregnancy, artesunate-mefloquine, dihydroartemisinin-piperaquine, hrp2 and hrp3 gene deletions.
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Files are hosted on the source repository. Click download to access the full dataset.