DOI: 10.6084/m9.figshare.21674321
title: Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

description: Data correct at time of upload (5 December 2022). Data maintained at https://www.malariagen.net/resource/34. This Figshare project provides information about the Pf7 dataset which contains genome variation data on over 20,000 worldwide samples of Plasmodium falciparum. The associated publication will be available from the above link once published. You can browse summary data using the Pf7 data exploration tool. <br> <strong>Background and previous releases</strong> This dataset is based on genome variation from the MalariaGEN network, including samples which were previously released through the Pf3k Project, Plasmodium falciparum Community Project and GenRe Mekong Project. It comprises multiple partner studies, each with its own research objectives and led by a local investigator. Genome sequencing is performed centrally, and partner studies are free to analyse and publish the genetic data produced on their own samples, in line with MalariaGEN’s guiding principles on equitable data sharing. This new open dataset is almost three times larger than the last dataset release (Pf6, published 2021), and includes samples from a wider geographic reach. The variants and genotypes described in this publication used version 3 of the analysis pipeline. Data produced using an earlier version of the data analysis pipeline can be explored using an interactive web application. <br> <strong>About the version 7 data pipeline</strong> Details of the methods can be found in the accompanying paper. <br> <strong>Content of the data release</strong> 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, (doi to be added on publication). 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. Drug resistance markers to inferred resistance status: details of the heuristics utilised to map genetic markers to resistance status classification. Genetic distances: Genetic distance matrix comparing all 20,864 samples. CRT haplotypes: Full crt gene haplotypes for 16,203 QC pass samples CSP C-terminal haplotypes:Full csp C-terminal haplotypes for 16,203 QC pass samples plus 6 lab strains. EBA175 calls: eba175 allelic type calls for 16,203 QC pass samples. Reference genome: the version of the 3D7 reference genome fasta file used for mapping. Annotation file: the version of the 3D7 reference annotation gff file used for genome annotations. Genetic distances: Genetic distance matrix comparing all 20,864 samples. (to be updated) Short variants genotypes: Genotype calls on 10,145,661 SNPs and short indels in all 20,864 samples from 33 countries, available both as VCF (to be updated) and zarr (to be updated) files. A README file describes in fine detail all the files included in the release, the format and interpretation of each column, and contains some tips and tricks for accessing genotype data in VCF and zarr files.