PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
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DOI：
10.1093/infdis/jit812
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发表时间：
2014-06-01
影响因子：
6.4
通讯作者：
Clark, Taane G.
中科院分区：
文献类型：
--
作者：
Preston, Mark D.;Assefa, Samuel A.;Clark, Taane G.
疟疾是一个全球性的公共卫生挑战，抗药性是控制和消除疾病的主要障碍。为了满足对更好的治疗和疫苗的迫切需要，需要对疟原虫生物学和疟疾流行病学有更深入的了解。对疟疾寄生虫基因组变异的更好了解，尤其是最毒力的恶性疟原虫（Pf）物种，有可能在这些领域产生新的见解。高通量测序和基因分型正在产生跨多个寄生虫种群的大量基因组数据。由此产生的识别信息变体，特别是单核苷酸多态性（SNP）的能力将导致发现群体内和群体间差异，从而能够开发用于诊断测定和临床研究的遗传条形码。了解耐药性和其他差异表型的遗传变异性也将有助于识别新的突变，并有助于监测和分层医学应用。PlasmoView交互式网络浏览工具使研究社区能够在地理环境中可视化基因组变异和注释（例如，生物功能）。第一个版本包含来自实验室菌株和四个疟疾流行地区（西非，东非，东南亚和大洋洲）的631个Pf分离株中的60多万个高质量SNP。
Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).