An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.
An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.
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DOI：
10.12688/wellcomeopenres.16168.2
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发表时间：
2021
影响因子：
--
通讯作者：
Ye H
中科院分区：
文献类型：
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作者：
MalariaGEN;Ahouidi A;Ali M;Almagro-Garcia J;Amambua-Ngwa A;Amaratunga C;Amato R;Amenga-Etego L;Andagalu B;Anderson TJC;Andrianaranjaka V;Apinjoh T;Ariani C;Ashley EA;Auburn S;Awandare GA;Ba H;Baraka V;Barry AE;Bejon P;Bertin GI;Boni MF;Borrmann S;Bousema T;Branch O;Bull PC;Busby GBJ;Chookajorn T;Chotivanich K;Claessens A;Conway D;Craig A;D'Alessandro U;Dama S;Day NP;Denis B;Diakite M;Djimdé A;Dolecek C;Dondorp AM;Drakeley C;Drury E;Duffy P;Echeverry DF;Egwang TG;Erko B;Fairhurst RM;Faiz A;Fanello CA;Fukuda MM;Gamboa D;Ghansah A;Golassa L;Goncalves S;Hamilton WL;Harrison GLA;Hart L;Henrichs C;Hien TT;Hill CA;Hodgson A;Hubbart C;Imwong M;Ishengoma DS;Jackson SA;Jacob CG;Jeffery B;Jeffreys AE;Johnson KJ;Jyothi D;Kamaliddin C;Kamau E;Kekre M;Kluczynski K;Kochakarn T;Konaté A;Kwiatkowski DP;Kyaw MP;Lim P;Lon C;Loua KM;Maïga-Ascofaré O;Malangone C;Manske M;Marfurt J;Marsh K;Mayxay M;Miles A;Miotto O;Mobegi V;Mokuolu OA;Montgomery J;Mueller I;Newton PN;Nguyen T;Nguyen TN;Noedl H;Nosten F;Noviyanti R;Nzila A;Ochola-Oyier LI;Ocholla H;Oduro A;Omedo I;Onyamboko MA;Ouedraogo JB;Oyebola K;Pearson RD;Peshu N;Phyo AP;Plowe CV;Price RN;Pukrittayakamee S;Randrianarivelojosia M;Rayner JC;Ringwald P;Rockett KA;Rowlands K;Ruiz L;Saunders D;Shayo A;Siba P;Simpson VJ;Stalker J;Su XZ;Sutherland C;Takala-Harrison S;Tavul L;Thathy V;Tshefu A;Verra F;Vinetz J;Wellems TE;Wendler J;White NJ;Wright I;Yavo W;Ye H
MalariaGEN是一个数据共享网络，使世界各地的团体能够在疟疾的基因组流行病学方面共同努力。在这里，我们描述了来自28个疟疾流行国家的疟疾agen合作研究的7000个恶性疟原虫样本的精心策划的基因组变异数据的新发布。使用标准化的分析管道，对300万个单核苷酸多态性（snp）和短索引进行了高质量的基因型调用。还分析了与耐药性相关的拷贝数变异和导致快速诊断试验失败的结构变异。几乎所有样本都显示出对至少一种抗疟药物具有耐药性的遗传证据，来自东南亚的一些样本携带对六种常用药物具有耐药性的标记。在寄生虫生命周期的蚊子阶段表达的基因在表现出强烈地理分化的位点中是突出的。通过继续扩大这一开放数据资源，我们的目标是促进对影响疟疾控制的进化过程的研究，并加速开发消除疟疾所需的监测工具包。
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 Plasmodium falciparum 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.