Sequencing and Genomics Cores

测序和基因组核心

基本信息

批准号：
8300973
负责人：
Sarah Kay Volkman
金额：
$ 17.22万
依托单位：
TULANE UNIVERSITY OF LOUISIANA
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-07-01 至 2017-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8300973
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 drug testing genetic analysis genetic variant genome sequencing genome wide association study genome-wide genotyping technology in vivo interest meetings melting next generation 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 publically 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.

基因组学核心将进行基因分型和群体遗传分析，以识别信息丰富的生物标志物对于本提案中的所有研究项目至关重要。本提案的共同主题是识别疟疾寄生虫、媒介和人类宿主的遗传变异，并将这种遗传变异与了解疟疾传播并制定有效的疟疾控制措施。全基因组寄生虫和载体的方法将提供发现遗传变异所需的信息与寄生虫耐药性和蚊子杀虫剂耐药性相关的信号。对与寄生虫耐药性、载体杀虫剂耐药性相关的特定位点进行基因分型，以及血红蛋白或其他与疟疾结果相关的人类基因座将告知干预措施的有效性旨在减少疟疾疾病负担。基因分型测定可识别患者样本中的寄生虫类型或随着干预策略的应用，将开发载体类型来跟踪这些人群的变化学习网站。基因分型核心将提供测序和基因分型资源以及分析确定这些人群中与干预反应相关的信息最丰富的标记的资源，疾病结果。基因组学核心将验证这些标记并开发可现场部署的检测方法低成本且易于实施，用于跟踪疟疾结果，作为消灭疟疾的干预策略疟疾的应用。共享资源基因组学核心的核心组成部分将涉及疾病培训流行国家科学家如何利用基因组序列和基因分型数据进行发现和工具随着社区范围内的努力增加公开测序和基因分型的数量疟疾寄生虫、按蚊媒介和人类宿主的数据，是能力建设和技术转让将是分析序列和基因分型数据所需的技能的发展，应用群体遗传学方法从这些数据中收集重要信号，以协助控制疟疾措施和监视。