{"doi":"10.12688/wellcomeopenres.16168.1","title":"An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples","abstract":"<ns3:p> MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 <ns3:italic>Plasmodium falciparum</ns3:italic> samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination. </ns3:p>","journal":"Wellcome Open Research","year":2021,"id":146732,"datarank":4.843488296597684,"base_score":5.293304824724492,"endowment":5.293304824724492,"self_citation_contribution":0.793995723708674,"citation_network_contribution":4.04949257288901,"self_endowment_contribution":0.793995723708674,"citer_contribution":4.04949257288901,"corpus_percentile":95.55968128722829,"corpus_rank":575,"citation_count":198,"citer_count":100,"citers_with_citation_signal":97,"citers_with_endowment":97,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.951,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.13388603"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":517884,"name":"Ambroise D. Ahouidi","orcid":"0000-0002-7009-8408","position":1,"is_corresponding":false},{"id":624712,"name":"Mozam Ali","orcid":null,"position":2,"is_corresponding":false},{"id":623657,"name":"Jacob Almagro‐Garcia","orcid":"0000-0002-0595-7333","position":3,"is_corresponding":false},{"id":623658,"name":"Alfred Amambua‐Ngwa","orcid":"0000-0003-4478-3601","position":4,"is_corresponding":false},{"id":238868,"name":"Chanaki Amaratunga","orcid":null,"position":5,"is_corresponding":false},{"id":236313,"name":"Roberto Amato","orcid":"0000-0001-8633-9221","position":6,"is_corresponding":false},{"id":444299,"name":"Lucas Amenga–Etego","orcid":"0000-0003-4468-0506","position":7,"is_corresponding":false},{"id":623659,"name":"Ben Andagalu","orcid":"0000-0002-8678-7478","position":8,"is_corresponding":false},{"id":579031,"name":"Tim Anderson","orcid":null,"position":9,"is_corresponding":false},{"id":623660,"name":"Voahangy Andrianaranjaka","orcid":"0000-0002-4881-8958","position":10,"is_corresponding":false},{"id":623661,"name":"Tobias O. Apinjoh","orcid":"0000-0001-9889-7271","position":11,"is_corresponding":false},{"id":623662,"name":"Cristina V. Ariani","orcid":"0009-0000-0887-5993","position":12,"is_corresponding":false},{"id":236331,"name":"Elizabeth A. Ashley","orcid":"0000-0002-7620-4822","position":13,"is_corresponding":false},{"id":476984,"name":"Sarah Auburn","orcid":"0000-0002-4638-536X","position":14,"is_corresponding":false},{"id":91455,"name":"Gordon A. Awandare","orcid":"0000-0002-8793-3641","position":15,"is_corresponding":false},{"id":623663,"name":"Hampaté Bâ","orcid":"0000-0002-9299-5775","position":16,"is_corresponding":false},{"id":623664,"name":"Vito Baraka","orcid":"0000-0001-9694-9293","position":17,"is_corresponding":false},{"id":341339,"name":"Alyssa E. Barry","orcid":"0000-0002-1189-2310","position":18,"is_corresponding":false},{"id":514666,"name":"Philip Bejon","orcid":"0000-0002-2135-7549","position":19,"is_corresponding":false},{"id":623665,"name":"Gwladys Bertin","orcid":"0000-0002-2218-9591","position":20,"is_corresponding":false},{"id":369689,"name":"Maciej F. Boni","orcid":"0000-0002-0830-9630","position":21,"is_corresponding":false},{"id":561820,"name":"Steffen Borrmann","orcid":"0000-0001-9189-4393","position":22,"is_corresponding":false},{"id":262843,"name":"Teun Bousema","orcid":"0000-0003-2666-094X","position":23,"is_corresponding":false},{"id":623666,"name":"OraLee H. Branch","orcid":"0000-0002-6720-6906","position":24,"is_corresponding":false},{"id":623667,"name":"Peter C. Bull","orcid":"0000-0002-7674-6752","position":25,"is_corresponding":false},{"id":530851,"name":"George Busby","orcid":"0000-0003-4148-6222","position":26,"is_corresponding":false},{"id":623668,"name":"Thanat Chookajorn","orcid":"0000-0003-2876-6203","position":27,"is_corresponding":false},{"id":236328,"name":"Kesinee Chotivanich","orcid":"0000-0002-6533-6811","position":28,"is_corresponding":false},{"id":623669,"name":"Antoine Claessens","orcid":"0000-0002-4277-0914","position":29,"is_corresponding":false},{"id":623670,"name":"David J. Conway","orcid":"0000-0002-8711-3037","position":30,"is_corresponding":false},{"id":328520,"name":"Alister Craig","orcid":"0000-0003-0914-6164","position":31,"is_corresponding":false},{"id":316972,"name":"Umberto D’Alessandro","orcid":"0000-0001-6341-5009","position":32,"is_corresponding":false},{"id":623671,"name":"Souleymane Dama","orcid":"0000-0002-5191-9207","position":33,"is_corresponding":false},{"id":236338,"name":"Nicholas Day","orcid":"0000-0003-2309-1171","position":34,"is_corresponding":false},{"id":624713,"name":"Brigitte Denis","orcid":null,"position":35,"is_corresponding":false},{"id":384668,"name":"Mahamadou Diakité","orcid":"0000-0002-4268-8857","position":36,"is_corresponding":false},{"id":260121,"name":"Abdoulaye Djimdé","orcid":"0000-0003-0062-2283","position":37,"is_corresponding":false},{"id":623672,"name":"Christiane Dolecek","orcid":"0000-0002-4635-9567","position":38,"is_corresponding":false},{"id":236340,"name":"Arjen M. Dondorp","orcid":"0000-0001-5190-2395","position":39,"is_corresponding":false},{"id":269829,"name":"Chris Drakeley","orcid":"0000-0003-4863-075X","position":40,"is_corresponding":false},{"id":550131,"name":"Eleanor Drury","orcid":"0000-0002-9887-6961","position":41,"is_corresponding":false},{"id":624714,"name":"Patrick Duffy","orcid":null,"position":42,"is_corresponding":false},{"id":472172,"name":"Diego F. Echeverry","orcid":null,"position":43,"is_corresponding":false},{"id":624715,"name":"Thomas G. Egwang","orcid":null,"position":44,"is_corresponding":false},{"id":590171,"name":"Berhanu Erko","orcid":"0000-0003-1685-752X","position":45,"is_corresponding":false},{"id":238878,"name":"Rick M. Fairhurst","orcid":null,"position":46,"is_corresponding":false},{"id":624716,"name":"Abdul Faiz","orcid":null,"position":47,"is_corresponding":false},{"id":236330,"name":"Caterina Fanello","orcid":"0000-0003-1932-9562","position":48,"is_corresponding":false},{"id":388477,"name":"Mark M. Fukuda","orcid":"0000-0001-5337-8937","position":49,"is_corresponding":false},{"id":378655,"name":"Dionicia Gamboa","orcid":"0000-0002-1420-7729","position":50,"is_corresponding":false},{"id":270630,"name":"Anita Ghansah","orcid":"0000-0003-4639-1249","position":51,"is_corresponding":false},{"id":503464,"name":"Lemu Golassa","orcid":"0000-0002-1216-8711","position":52,"is_corresponding":false},{"id":236314,"name":"Sónia Gonçalves","orcid":"0000-0003-0321-3303","position":53,"is_corresponding":false},{"id":623673,"name":"William L. Hamilton","orcid":"0000-0002-3330-353X","position":54,"is_corresponding":false},{"id":624717,"name":"G. L. Abby Harrison","orcid":null,"position":55,"is_corresponding":false},{"id":623674,"name":"Lee Hart","orcid":"0000-0002-6473-0964","position":56,"is_corresponding":false},{"id":551165,"name":"Christa Henrichs","orcid":null,"position":57,"is_corresponding":false},{"id":623675,"name":"Tran Tinh Hien","orcid":"0000-0002-2383-4791","position":58,"is_corresponding":false},{"id":623676,"name":"Catherine A. Hill","orcid":"0000-0001-5727-6356","position":59,"is_corresponding":false},{"id":623677,"name":"Abraham Hodgson","orcid":"0009-0003-0700-1364","position":60,"is_corresponding":false},{"id":530850,"name":"Christina Hubbart","orcid":"0000-0001-9576-9581","position":61,"is_corresponding":false},{"id":623678,"name":"Mallika Imwong","orcid":"0000-0003-0857-1855","position":62,"is_corresponding":false},{"id":270624,"name":"Deus S. Ishengoma","orcid":"0000-0003-2040-3416","position":63,"is_corresponding":false},{"id":448943,"name":"Scott A. 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Johnson","orcid":"0000-0002-6365-906X","position":68,"is_corresponding":false},{"id":103497,"name":"Dushyanth Jyothi","orcid":"0000-0002-0448-5303","position":69,"is_corresponding":false},{"id":623680,"name":"Claire Kamaliddin","orcid":"0000-0001-8198-6235","position":70,"is_corresponding":false},{"id":623681,"name":"Edwin Kamau","orcid":"0000-0002-5761-7883","position":71,"is_corresponding":false},{"id":556605,"name":"Mihir Kekre","orcid":null,"position":72,"is_corresponding":false},{"id":624719,"name":"Krzysztof Henryk Kluczynski","orcid":null,"position":73,"is_corresponding":false},{"id":623682,"name":"Theerarat Kochakarn","orcid":"0000-0002-3524-8079","position":74,"is_corresponding":false},{"id":624720,"name":"Abibatou Konaté","orcid":null,"position":75,"is_corresponding":false},{"id":33751,"name":"Dominic Kwiatkowski","orcid":"0000-0002-5023-0176","position":76,"is_corresponding":false},{"id":310071,"name":"Myat Phone Kyaw","orcid":null,"position":77,"is_corresponding":false},{"id":535403,"name":"Pharath Lim","orcid":"0000-0002-1012-2461","position":78,"is_corresponding":false},{"id":290868,"name":"Chanthap Lon","orcid":"0000-0003-4901-5003","position":79,"is_corresponding":false},{"id":623683,"name":"Kovana Marcel Loua","orcid":"0000-0003-0571-0944","position":80,"is_corresponding":false},{"id":623684,"name":"Oumou Maïga‐Ascofaré","orcid":"0000-0003-2947-5651","position":81,"is_corresponding":false},{"id":88410,"name":"Claudio Malangone","orcid":"0000-0003-1639-8589","position":82,"is_corresponding":false},{"id":623685,"name":"Magnus Manske","orcid":"0000-0001-5916-0947","position":83,"is_corresponding":false},{"id":623686,"name":"Jutta Marfurt","orcid":"0000-0002-3846-0825","position":84,"is_corresponding":false},{"id":623687,"name":"Kevin Marsh","orcid":"0000-0001-8377-5466","position":85,"is_corresponding":false},{"id":236332,"name":"Mayfong Mayxay","orcid":"0000-0002-6056-4516","position":86,"is_corresponding":false},{"id":326561,"name":"Alistair Miles","orcid":"0000-0001-9018-4680","position":87,"is_corresponding":false},{"id":236336,"name":"Olivo Miotto","orcid":"0000-0001-8060-6771","position":88,"is_corresponding":false},{"id":623688,"name":"Victor A. Mobegi","orcid":"0000-0002-1962-5583","position":89,"is_corresponding":false},{"id":623689,"name":"Olugbenga Ayodeji Mokuolu","orcid":"0000-0001-8273-5876","position":90,"is_corresponding":false},{"id":621328,"name":"Jacqui Montgomery","orcid":"0000-0003-3404-9024","position":91,"is_corresponding":false},{"id":283141,"name":"Ivo Müeller","orcid":"0000-0001-6554-6889","position":92,"is_corresponding":false},{"id":236333,"name":"Paul N. 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[majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Underlying data ... Data are also available from Figshare. Figshare: Supplementary data to: An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. https:// doi.org/10.6084/m9.figshare.13388603.","grounded":false,"rationale":"The statement points to a repository record (Figshare) with a DOI. 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Figshare: Supplementary data to: An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. https:// doi.org/10.6084/m9.figshare.13388603.","grounded":false,"rationale":"The dataset identifier appears only in the body text, not in the reference list. 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[downgraded to 'partial' — no verifiable quote from the paper]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Data hosted with Figshare are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).","grounded":false,"rationale":"The paper explicitly labels the data's access level as CC-BY 4.0, which is an open access licence. 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"We used the Illumina platform to produce genome sequencing data on all samples and we mapped the sequence reads against the P. falciparum 3D7 v3 reference genome.","grounded":false,"rationale":"The paper names the specific platform (Illumina) and reference genome version used for data production. 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[downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","anchors":["RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'","NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given for the primary dataset; the Figshare supplementary data have a version in the reference list, but the main dataset is not versioned. [majority verdict 'no' (2/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"custom java code (available at https://github.com/malariagen/GeneticReportCard)","grounded":false,"rationale":"The paper provides a GitHub repository URL for custom code used in the analysis. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for any external resource is provided in the text.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state how long the data will be retained or committed to persistence.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. 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'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. 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