Identification of Rare Variants in PD through Whole Exome Sequencing

通过全外显子组测序鉴定 PD 罕见变异

• 批准号: 8264601
• 负责人: JEFFERY Marvin VANCE
• 金额: $ 68.01万
• 依托单位: UNIVERSITY OF MIAMI SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-30 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8264601
• 关键词: Age; Amish; Candidate Disease Gene; Cell Culture Techniques; Cells; Chromosomes; Chromosomes, Human, Pair 9; Cluster Analysis; Complex; Data; Data Set; Disease; Environmental Exposure; Fission Yeast; Frequencies; Gene Cluster; Gene Expression Profile; Gene Frequency; Gene Silencing; Genes; Genetic; Goals; Growth; Individual; Mitochondria; Modeling; Mutation; Nuclear; Nucleic Acid Regulatory Sequences; Odds Ratio; Organism; Parkinson Disease; Pathway interactions; Patients; Population; Recording of previous events; Research; Risk; Sample Size; Sampling; Techniques; Testing; Universities; Variant; Work; Yeasts; Zebrafish; biological systems; cost; disorder control; exome; gene discovery; gene function; genetic linkage analysis; genetic pedigree; genome sequencing; genome wide association study; genome-wide; improved; induced pluripotent stem cell; interest; meetings; next generation; tool

Project I - 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 there 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.

项目I-帕金森病(PD)的遗传学研究已经成为推动 研究方面的增长。然而，越来越多的人意识到，仅常见的变异(MAF&GT；5%)就是 对发生帕金森病和许多其他复杂疾病的风险的遗传贡献不负责任。 对于这种缺失的基因贡献，另一种假说是罕见的变异。在过去一年里 我们发起了首批帕金森病全外显子组测序(WES)项目之一，以寻找 导致帕金森病的罕见变异。这个项目继续了这项工作，结合了我们最近在路径上的工作 并将提供有关已发现基因的途径和功能的信息。 具体目标1在500个发现集中发现一组稀有变异和额外的SNP 帕金森病患者和500名对照，用于在我们的复制数据集中进行特定目标3a的测试。 特定目标2利用一个庞大的阿米什血统来寻找罕见的变异，使用WES，定向捕获和 潜在的全基因组测序。阿米什人呈现出一群既有相对 统一的环境暴露史和增加的遗传同质性。连锁分析揭示了一个 在9号染色体上的几个分支上有强基因座，在其他几个分支上有额外的基因座 染色体。因此，这是研究远交群体中帕金森病的一个很好的模型。在特定的目标3中，我们将测试 来自我们发现的数据集的前200个基因和/或变体在另外500个病例和500个对照中。 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。分析了 该验证数据集将包括数据的多个子集，包括按变体、基因内的变体 “簇”，途径分析，感兴趣的基因网络，如线粒体核基因和Aao 不同之处。为了改善有关通路的信息，并评估已识别的基因和 与其他已知PD基因的关系，我们将使用沉默和其他 通过核心D对三个不同生物系统中的候选基因进行干预的技术： 来自帕金森病患者和对照组的酵母、斑马鱼和诱导的多能干细胞。