Genetics of Parkonsonism

帕金森症的遗传学

• 批准号: 8540539
• 负责人: JEFFERY Marvin VANCE
• 金额: $ 7.65万
• 依托单位: UNIVERSITY OF MIAMI SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-15 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8540539
• 关键词: Affect; Age; Amish; Applied Genetics; Area; Bioinformatics; Biological; Biological Markers; Brain; Candidate Disease Gene; Cells; Cholecalciferol; Chromosomes; Chromosomes, Human, Pair 9; Clinical; Code; Coffee; Community Health Education; Complex; DNA Sequence; Data; Data Analyses; Data Set; Disease; Doctor of Philosophy; Early Diagnosis; Early treatment; Environmental Exposure; Epidemiologist; Etiology; Evaluation; Frequencies; Gene Cluster; Gene Expression Regulation; Genes; Genetic; Genetic Predisposition to Disease; Genetic Research; Genomics; Goals; Growth; Human; Image; Individual; Institutes; Intervention; Mission; Mitochondria; Modeling; Molecular; Mutation; Nuclear; Parkinson Disease; Pathway interactions; Patients; Pesticides; Pharmaceutical Preparations; Pharmacogenetics; Pharmacotherapy; Population; Predisposition; Preventive; Principal Investigator; Proteins; Protocols documentation; RNA; RNA Sequences; Recording of previous events; Research; Research Infrastructure; Resources; Risk; Risk Factors; Role; Sampling; Series; Smoking; Symptoms; Techniques; Technology; Testing; Therapeutic; Training; Translating; Variant; Vision; Vitamin D; Work; Yeasts; Zebrafish; base; biological systems; clinical phenotype; cost; data management; disorder risk; environmental agent; epigenomics; exome; gene discovery; gene function; genetic linkage analysis; genetic pedigree; genome sequencing; genome wide association study; genome-wide; high risk; improved; induced pluripotent stem cell; innovation; insight; interest; multidisciplinary; nervous system disorder; next generation; prevent; programs; skills; success; therapeutic target; tool

DESCRIPTION (provided by applicant): The overall goal of the center is to identify genes or genetic mechanisms that cause or contribute to an individual's susceptibility to Parkinson Disease (PD) and to translate these discoveries into early detection of risk or disease, as well as provide therapeutic targets for PD. Our long-term goals include improving therapy for patients by providing important genes, genetic mechanisms and pathways that may be useful to target with drug treatment or other intervention to slow the disease. Project 1 "Identification of rare variants (RV) in PD through whole exome sequencing (WES)" continues our work from the previous year in at total of 1000 PD patients and 1000 controls. The number of genes which have reached genome-wide significance through genome wide association studies (GWAS) remains small and with small effect. This has led to the hypothesis that there is a missing genetic component. The most likely candidate for this missing "hereditability" has been suggested to be rare variants. Pathway analyses and gene network analyses will be included with more traditional frequency analyses. Project 2 " Long ncRNAs as epigenomic modulators and CSF biomarkers in PD" brings an exciting new area of research to PD. Recent RNA sequencing studies have shown that a large proportion of RNA produced by the cell comes from DNA sequence that does not code for protein (ncRNA). Recent work has shown an important role in the regulation of gene expression by ncRNAs in neurological disease. This project seeks to identify key ncRNAs that contribute to the etiology of PD and could serve as biomarkers of disease in CSF. Project 3 "Vitamin D concentration, genetic modifiers, and PD" is a study of the pharmacogenetics of Vitamin D (ViD). Studies have suggested that low ViD is a risk factor for PD. This study seeks to confirm this in a large dataset, and define the gene-ViD interactions that will be necessary if it is to become preventive therapy. The Center has 4 cores: (A) Administrative with Education and Community functions (B) Clinical Resource Core, (C) Statistical Analysis and Bioinformatics Core and (D) a new and innovative core, the Disease IVIodeling Core using yeast, zebrafish and induced pluripotent stem cells. PROJECT 1 Principal Investigator: Jeffery M. Vance, MD, PhD Title: Identification of Rare Variants in PD through Whole Exome Sequencing Description (provided by applicant): Genetic studies in Parkinson Disease (PD) have been a major tool fueling the tremendous growth in research. However, there is increasing realization that common variations (MAF > 5%) alone are not responsible for the genetic contribution to risk for developing PD and many other complex disorders. One of the alternative hypothesis for this missing genetic contribution are rare variants. Over the past year we initiated one of the first whole exome sequencing (WES) projects for Parkinson disease to search for rare variants contributing to PD. This project continues this work, incorporates our recent work on pathways into our analyses, and will provide information on the pathways and function of the genes discovered. Specific Aim 1 identifies an initial set of rare variants and additional SNPs in a discovery set of 500 Parkinson Disease patients and 500 controls for testing in our replication dataset in Specific Aim 3a. Specific Aim 2 utilizes a large Amish pedigree to look for rare variants using WES, targeted capture and potentially whole genome sequencing. The Amish present a group of individuals with both a relatively uniform environmental exposure history and increased genetic homogeneity. Linkage analysis reveals a strong locus on chromosome 9 In several branches of the pedigree, and additional loci on other chromosomes. This is thus a good model for PD in the outbred population. In Specific Aim 3 we will test the top 200 genes and/or variants from our discovery dataset in an additional 500 cases and 500 controls. To accomplish this efficiently we will create a targeted capture for next generation sequencing. Analyses of this verification datasets will include multiple subsets of the data including by variant, variants within a gene "cluster", pathway analyses, gene networks of interest such as mitochondrial nuclear genes and AAO differences. In order to improve information on pathways and also evaluate the identified genes and their relationship to other known PD genes, we will examine differentially expression using silencing and other interventional techniques for the candidate genes in three different biological systems through Core D: yeast, zebrafish and induced pluripotent stem cells derived from PD patients and controls.

描述(由申请人提供)：该中心的总体目标是确定导致或促成个人易患帕金森病(PD)的基因或遗传机制，并将这些发现转化为风险或疾病的早期发现，以及为PD提供治疗靶点。我们的长期目标包括通过提供重要的基因、遗传机制和途径来改善患者的治疗，这些基因、遗传机制和途径可能有助于药物治疗或其他干预措施来减缓疾病。项目1“通过全外显子组测序(WES)鉴定PD中的稀有变异(RV)”继续了我们从前一年开始的工作，总共有1000名PD患者和1000名对照。通过全基因组关联研究达到全基因组意义的基因数量仍然很少，影响也很小。这导致了一种假设，即存在缺失的基因成分。这种缺失的“遗传性”最有可能的候选者是罕见的变种。途径分析和基因网络分析将包括在更传统的频率分析中。项目2《作为帕金森病表观基因组调节剂和脑脊液生物标志物的长ncRNAs》为帕金森病带来了一个令人兴奋的新研究领域。最近的RNA测序研究表明，细胞产生的RNA中有很大一部分来自不编码蛋白质的DNA序列(NcRNA)。最近的研究表明，在神经系统疾病中，ncRNAs在基因表达调控中发挥着重要作用。该项目旨在确定与帕金森病病因有关的关键ncRNAs，并可能作为脑脊液中疾病的生物标记物。项目3“维生素D浓度、遗传修饰剂和PD”是维生素D(VID)的药物遗传学研究。研究表明，低VID是帕金森病的危险因素。这项研究试图在一个大型数据集中证实这一点，并定义如果它要成为预防性治疗所必需的基因-VID相互作用。该中心有四个核心：(A)具有教育和社区职能的行政核心(B)临床资源核心，(C)统计分析和生物信息学核心，以及(D)使用酵母、斑马鱼和诱导多能干细胞的新的创新核心--疾病试管重建核心。 项目1 主要研究员：杰弗里·M·万斯，医学博士 通过全外显子组测序鉴定帕金森病罕见变异 描述(由申请人提供)：帕金森病(PD)的基因研究一直是推动研究巨大增长的主要工具。然而，越来越多的人意识到，普通变异(MAF&GT；5%)本身并不是导致帕金森病和许多其他复杂疾病风险的遗传因素。对于这种缺失的基因贡献，另一种假说是罕见的变异。在过去的一年里，我们启动了针对帕金森病的首批完整外显子组测序(WES)项目之一，以寻找导致帕金森病的罕见变异。该项目继续这项工作，将我们最近在通路方面的工作纳入到我们的分析中，并将提供有关所发现基因的通路和功能的信息。特定目标1在由500名帕金森病患者和500名对照组成的发现集中确定了最初的一组罕见变异和额外的SNPs，以便在我们的特定目标3a的复制数据集中进行测试。特殊目的2利用一个庞大的阿米什血统，使用WES、靶向捕获和潜在的全基因组测序来寻找罕见的变异。阿米什人表现出一群既有相对一致的环境暴露史，又有更高的遗传同质性的个体。连锁分析表明，在该家系的几个分支中，在9号染色体上有一个很强的基因座，在其他染色体上也有额外的基因座。因此，这是研究远交群体中帕金森病的一个很好的模型。在具体目标3中，我们将在另外500个病例和500个对照中测试我们发现的数据集的前200个基因和/或变体。为了有效地实现这一点，我们将为下一代测序创建一个有针对性的捕获。对这种验证数据集的分析将包括数据的多个子集，包括按变种、基因“簇”内的变种、路径分析、感兴趣的基因网络，如线粒体核基因和Aao差异。为了提高对通路的信息，也为了评估已识别的基因及其与其他已知PD基因的关系，我们将通过核心D：酵母、斑马鱼和来自PD患者和对照的诱导多能干细胞，利用沉默和其他干预技术来检测候选基因在三个不同生物系统中的差异表达。