Genome-wide studies to identify markers of artemisinin-resistant malaria

描述(由申请人提供)： 世界各地都在使用以青蒿素为基础的高效抗疟疾药物，这些药物有助于减轻许多地区的疟疾负担。柬埔寨西部出现了具有青蒿素抗药性的恶性疟原虫，它的潜在传播有可能逆转最近在防治疟疾方面取得的成果，并使新一轮全球根除运动的计划流产。由于缺乏工具来衡量其传播的程度和方向，目前遏制青蒿素抗药性疟疾的努力受到阻碍。目前，只有费力的临床试验才能可靠地测量耐药性。检测青蒿素耐药性标记的分子检测将是一种非常有价值的监测工具，但耐药性的遗传基础尚不清楚。我们提出了全基因组关联研究(GWAS)，旨在确定可用于在青蒿素抗性寄生虫全球传播之前跟踪和遏制它们的分子标记。这项工作将通过两个目标来完成。首先，我们将使用一组密集的单核苷酸多态(SNPs)来定位恶性疟原虫基因组与青蒿素耐药性相关的区域。为了实现这一目标，我们将使用已建立的SNP调用渠道，从完成青蒿素疗效试验期间收集的寄生虫短读测序数据中确定~421,000个SNPs的基因型，并估计寄生虫基因型与青蒿素治疗后将寄生虫血症减少一半所需时间(即寄生虫清除半衰期)之间的关联。将在两个独立的样本集中评估相关性，并将进行荟萃分析以验证与青蒿素耐药性相关的基因组区域。在第二个目标中，我们将确定目标1中确定的基因组区域内的候选基因并确定其优先顺序，并使用下一代测序数据来确定高优先级基因中的多态及其与寄生虫清除半衰期的关联。如果成功，该项目将导致开发一种快速检测方法，在随后的候选基因关联研究中检测青蒿素耐药性的候选标记，以及开始对候选基因进行功能表征以更好地了解耐药性的机制的数据。

DESCRIPTION (provided by applicant): Highly effective artemisinin-based antimalarial drugs are used worldwide and have contributed to reductions in the malaria burden in many areas. Artemisinin-resistant Plasmodium falciparum malaria has emerged in western Cambodia and its potential spread threatens to reverse recent gains against malaria and to abort plans for a renewed global eradication campaign. Ongoing efforts to contain artemisinin-resistant malaria are hampered by the lack of tools to gauge the extent and direction of its spread. Presently, only laborious clinical trials can reliably measure resistance. A molecular assay to detect markers of artemisinin resistance would be a highly valuable surveillance tool, but the genetic basis of resistance is unknown. We propose genome-wide association studies (GWAS) that aim to identify molecular markers that can be used to track and contain artemisinin-resistant parasites before they spread globally. The work will be accomplished in two aims. First, we will use a dense panel of single nucleotide polymorphisms (SNPs) to map regions of the P. falciparum genome that are associated with artemisinin resistance. To accomplish this, we will use an established SNP- calling pipeline to determine genotypes at ~421,000 SNPs from short-read sequencing data in parasites collected during completed trials of artemisinin efficacy, and we will estimate the association between parasite genotypes and the amount of time it takes to reduce parasitemia by half following artemisinin treatment (i.e. parasite clearance half-life). Associations will be estimated in two independent sample sets, and meta-analysis will be performed to validate genomic regions associated with artemisinin resistance. In the second aim, we will identify and prioritize candidate genes within genomic regions identified in Aim 1 and use next-generation sequencing data to identify polymorphisms within high-priority genes and their association with parasite clearance half-life. If successful, this project will result in the development of a rapid assay to detect candidate markers of artemisinin resistance in subsequent candidate gene association studies, as well as data to begin the functional characterization of candidate genes to better understand the mechanisms underlying resistance.