Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

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. Background and previous releases 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. About the version 7 data pipeline Details of the methods can be found in the accompanying paper. 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, (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.本数据截至上传时（2022年12月5日）准确有效。数据维护地址为https://www.malariagen.net/resource/34。本Figshare（Figshare）项目提供Pf7数据集的相关信息，该数据集包含全球超过20000份恶性疟原虫（Plasmodium falciparum）样本的基因组变异数据。相关研究论文将于上述链接发布后正式公开。用户可通过Pf7数据探索工具浏览汇总数据。 背景与既往版本 本数据集基于疟疾基因组网络（MalariaGEN）的基因组变异数据，包含此前通过Pf3k项目、恶性疟原虫社区项目（Plasmodium falciparum Community Project）及GenRe Mekong项目发布的样本。本数据集由多个合作研究项目组成，每个项目均设有独立研究目标，由当地研究负责人主导。基因组测序工作集中完成，合作研究方可按照MalariaGEN关于公平数据共享的指导原则，自由分析并发布其自有样本产生的遗传数据。本全新开放数据集规模较2021年发布的上一版本（Pf6）扩大近两倍，且覆盖了更广泛的地理区域。本论文中描述的变异与基因型采用第3版分析流程生成。使用早期数据分析流程生成的数据，可通过交互式Web应用程序进行探索。 第7版数据流程说明 具体方法细节可参见随附研究论文。 数据发布内容 本发布包包含合作研究项目详情、样本元数据及从基因组数据中推断出的关键样本属性，还包含包括原始序列读数在内的基因组数据。更多细节与分析结果可参见随附的数据发布论文。本数据为开放获取资源。使用本数据的出版物需按照以下格式致谢并引用数据来源：“本出版物使用MalariaGEN数据，详见《Pf7：全球20000份恶性疟原虫基因组变异开放数据集》，MalariaGEN等，（发布时将补充DOI）。” 研究项目信息：82个合作研究项目的详细信息，包括项目描述、联系方式及核心参与人员。 样本来源与测序元数据：涵盖20864份来自33个国家的样本信息，包括合作研究项目信息、采集地点与年份、欧洲核苷酸档案库（European Nucleotide Archive, ENA）登录号以及质量控制（Quality Control, QC）信息。 感染复杂性度量：对16203份通过QC的样本的宿主内多样性（FWS）进行了表征。 抗药性标记基因型：针对16203份样本的已知抗药性标记基因型进行分析，包含6个基因座的氨基酸与拷贝数基因型：crt、dhfr、dhps、mdr1、kelch13、plasmepsin 2-3。 推断的抗药性状态分类：将16203份通过QC的样本分为对10种药物/药物组合及快速诊断试验（Rapid Diagnostic Test, RDT）检测的不同抗药性类型，涉及：氯喹、乙胺嘧啶、磺胺多辛、甲氟喹、青蒿素、哌喹、治疗无并发症疟疾的磺胺多辛-乙胺嘧啶、妊娠期间歇性预防治疗用磺胺多辛-乙胺嘧啶、青蒿琥酯-甲氟喹、双氢青蒿素-哌喹，以及hrp2和hrp3基因缺失。 抗药性标记到抗药性状态的映射：详述了用于将遗传标记映射至抗药性状态分类的启发式规则。 遗传距离矩阵：用于比对全部20864份样本的遗传距离矩阵。 crt基因单倍型：16203份通过QC的样本的完整crt基因单倍型。 C端CSP单倍型：16203份通过QC的样本及6株实验室菌株的完整csp C端单倍型。 EBA175分型调用：16203份通过QC的样本的eba175等位基因类型调用结果。 参考基因组：用于序列比对的3D7参考基因组fasta文件版本。 注释文件：用于基因组注释的3D7参考注释gff文件版本。 遗传距离矩阵（待更新）：用于比对全部20864份样本的遗传距离矩阵。 短变异基因型：对来自33个国家的20864份样本中的10145661个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）与短插入缺失（insertion-deletion, indel）进行基因型调用，相关数据以VCF（待更新）与zarr（待更新）格式提供。 README文件：本发布包附带的README文件将详细说明本次发布包含的所有文件、各列的格式与解读方法，并提供访问VCF及zarr格式基因型数据的技巧与提示。