Sequencing and Genomics Cores

测序和基因组核心

基本信息

批准号：
8691370
负责人：
Sarah Kay Volkman
金额：
$ 18.83万
依托单位：
TULANE UNIVERSITY OF LOUISIANA
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/8691370
关键词：
Accounting Africa African Algorithms Alleles Anopheles Genus Anopheles gambiae Antimalarials Base Pairing Biological Assay Biological Markers Blood specimen Budgets Chromosomes Classification Clinical Clinical Treatment Collection Communities Complex Computer software Country Culicidae DNA DNA Resequencing DNA Sequencing Facility Data Data Analyses Data Quality Data Set Development Disease Outcome Drug resistance Effectiveness of Interventions Endemic Diseases Environment Evaluation Failure Female Freezing Frequencies Gene Frequency Genetic Genetic Drift Genetic Materials Genetic Polymorphism Genetic Variation Genome Genomics Genomics Shared Resource Genotype Glean Goals Haplotypes Hemoglobin Human In Vitro Individual Infection Insecticide Resistance Insecticides Institutes Intervention Investigation Left Length Libraries Linkage Disequilibrium Malaria Maps Measures Methodology Methods Minor Modeling Monitor Morphologic artifacts Natural Selections Neighborhoods Nucleic Acids Organism Outcome Paper Parasite resistance Parasites Patients Pattern Pharmaceutical Preparations Phenotype Plasmodium falciparum Population Population Genetics Population Study Principal Component Analysis Procedures Process Public Health Schools Reading Reagent Refractory Relative (related person)Reporting Research Research Project Grants Research Proposals Resistance Resolution Resource Sharing Resources Sample Size Sampling Scientist Seasons Sentinel Sequence Analysis Signal Transduction Single Nucleotide Polymorphism Site Stratification Structure Technology Technology Transfer Testing Time Training Treatment Failure Validation Variant Weight base burden of illness cost deep sequencing drug testing genetic analysis genetic variant genome sequencing genome wide association study genome-wide genotyping technology in vivo interest meetings melting next generation sequencing novel novel marker parasite genome population based pressure programs response skills statistics tool tool development transmission process treatment response validation studies vector

项目摘要

The Genomics Core will carry out the genotyping and population genetic analysis required to identify informative biomarkers fundamental to all research projects in this proposal. A common theme of this proposal is to identify genetic variation in the malaria parasite, vector and human host and relate this genetic variation to understanding malaria transmission and development of effective malaria control measures. Whole genome approaches for both the parasite and vector will provide genetic variation Information necessary to discover signals associated with drug resistance in the parasite and insecticide resistance in the mosquito. Genotyping specific loci related to drug resistance in the parasite, insecticide resistance in the vector, and hemoglobin or other human loci associated with malaria outcome, will inform the effectiveness of interventions directed at reducing malaria disease burden. Genotyping assays to identify parasite types in patient samples or vector types will be developed to track changes in these populations as intervention strategies are applied at the study sites. The genotyping core will provide sequencing and genotyping resources, as well as analysis resources to determine the most informative markers in these populations related to intervention response and disease outcome. The Genomics Core will validate these markers and develop field-deployable assays that are low-cost and easy to Implement for tracking malaria outcomes as intervention strategies toward the eradication of malaria are applied. A central component of the shared resources Genomics Core will involve training disease endemic country scientists how to leverage genomic sequence and genotyping data for both discovery and tool development As community-wide efforts increase the amount of publicly available sequencing and genotyping data for the malaria parasite, the anopheles vector, and the human host, an opportunity of capacity building and technology transfer will be the development of skills necessary to analyze sequence and genotyping data and apply population genetic approaches to glean important signals from these data to assist with malaria control measures and surveillance.

基因组核心将进行基因分型和种群遗传分析，以鉴定本提案中所有研究项目基础的信息生物标志物。该提议的共同主题是确定疟疾寄生虫，载体和人宿主的遗传变异，并将这种遗传变异与了解疟疾的传播和开发有效的疟疾控制措施。全基因组寄生虫和向量的方法都将提供发现必要的遗传变异信息与寄生虫耐药性和蚊子耐药性相关的信号。基因分型特异性基因座与寄生虫的耐药性有关，载体中的杀虫剂耐药性，以及血红蛋白或其他与疟疾结局相关的人类基因座将为干预的有效性提供信息致力于减轻疟疾疾病负担。基因分型测定以识别患者样本中的寄生虫类型或将开发向量类型以跟踪这些人群的变化，因为在研究地点。基因分型核心将提供测序和基因分型资源，并分析确定与干预响应和疾病结果。基因组学核心将验证这些标记，并开发可替代的测定法低成本且易于实施以跟踪疟疾结果作为消除的干预策略应用疟疾。共享资源基因组学核心的核心组成部分将涉及训练疾病特有国家科学家如何利用发现和工具的基因组序列和基因分型数据随着社区范围的努力的发展增加了公开可用的测序和基因分型疟疾寄生虫，肛门载体和人类宿主的数据，这是能力建设和技术转移将是分析序列和基因分型数据所必需的技能的发展将种群遗传方法应用于这些数据中的重要信号以帮助控制疟疾措施和监视。