An online mapping database of molecular markers of drug resistance in Plasmodium falciparum: the ACT Partner Drug Molecular Surveyor
An online mapping database of molecular markers of drug resistance in Plasmodium falciparum: the ACT Partner Drug Molecular Surveyor
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DOI：
10.1186/s12936-019-2645-x
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发表时间：
2019-01-18
期刊：
影响因子：
3
通讯作者：
Humphreys, Georgina S.
中科院分区：
文献类型：
--
作者：
Otienoburu, Sabina Dahlstroem;Suay, Ignacio;Humphreys, Georgina S.
背景在此项目之前，只有少数在线可视化存在探索抗疟药物耐药性的分子标记物的已发表文献，没有专门针对与恶性疟原虫对青蒿素为基础的联合治疗（ACT）中的伙伴药物的耐药性相关的标记物。在不同设计的研究中收集分子信息，使用各种分子方法学和数据分析策略，使得难以进行跨研究比较。该项目的目的是开发一个免费的在线工具，将广泛发表的抗疟药物耐药性分子标记数据可视化，从与三种最常见的伙伴药物耐药性有关的两个基因pfcrt和pfmdr-1开始;阿莫地喹、苯芴醇和甲氟喹。方法进行文献综述，并使用标准化方法从出版物中提取数据，并做出了有关可视化的关键决策。建立了一个全球地理空间数据库，包含pfmdr 1和pfcrt单核苷酸多态性以及pfmdr 1拷贝数变异。一个信息学框架的开发，使灵活的开发工具随着时间的推移和有效的适应不同的源data.ResultsThe数据库讨论了本文中的PFMDR 1和PFCRT标记的患病率信息，从579个地理位置在76个不同的国家，包括结果从超过86,000个样本从2001年1月至2017年5月发表的456篇文章。ACT Partner Drugs Molecular Surveyor于2015年3月由全球抗疟药耐药网络（WWARN）推出，自那时以来已吸引了3000多名独立访问者。这里介绍的是如何探索的Surveyor数据库，以监测分子标记物的流行率的本地，时间的变化示范。此处包含截至2017年5月的出版物，但在线ACT合作药物分子调查员会不断更新新数据和相关标志物。结论WWARN ACT合作药物分子调查员总结了pfmdr 1和pfcrt基因中耐药标志物的数据。该数据库完全可以访问，为用户提供了丰富的资源来探索和分析，从而为不同的目的利用集中的标准化数据库。这一开放源码软件框架可适用于其他数据，随后推出的青蒿素分子探测器和间日疟探测器就证明了这一点。
BackgroundPrior to this project, only a handful of online visualizations existed for exploring the published literature on molecular markers of antimalarial drug resistance, and none specifically for the markers associated with Plasmodium falciparum resistance to the partner drugs in artemisinin-based combination therapy (ACT). Molecular information is collected in studies with different designs, using a variety of molecular methodologies and data analysis strategies, making it difficult to compare across studies. The purpose of this project was to develop a free online tool, which visualizes the widely published data on molecular markers of antimalarial drug resistance, starting with the two genes pfcrt and pfmdr-1, associated with resistance to the three most common partner drugs; amodiaquine, lumefantrine and mefloquine.MethodsA literature review was conducted, and a standardized method was used to extract data from publications, and critical decisions on visualization were made. A global geospatial database was developed of specific pfmdr1 and pfcrt single nucleotide polymorphisms and pfmdr1 copy number variation. An informatics framework was developed that allowed flexibility in development of the tool over time and efficient adaptation to different source data.ResultsThe database discussed in this paper has pfmdr1 and pfcrt marker prevalence information, from 579 geographic sites in 76 different countries, including results from over 86,000 samples from 456 articles published January 2001-May 2017. The ACT Partner Drugs Molecular Surveyor was launched by the WorldWide Antimalarial Resistance Network (WWARN) in March 2015 and it has attracted over 3000 unique visitors since then. Presented here is a demonstration of how the Surveyor database can be explored to monitor local, temporal changes in the prevalence of molecular markers. Here publications up to May 2017 were included, however the online ACT partner drug Molecular Surveyor is continuously updated with new data and relevant markers.ConclusionsThe WWARN ACT Partner Drugs Molecular Surveyor summarizes data on resistance markers in the pfmdr1 and pfcrt genes. The database is fully accessible, providing users with a rich resource to explore and analyze, and thus utilize a centralized, standardized database for different purposes. This open-source software framework can be adapted to other data, as demonstrated by the subsequent launch of the Artemisinin Molecular Surveyor and the Vivax Surveyor.