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: 8540540
• 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: 2012
• 资助国家: 美国
• 起止时间: 2012-09-15 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8540540
• 关键词: Age; Amish; Candidate Disease Gene; Chromosomes; Chromosomes, Human, Pair 9; Cluster Analysis; Complex; Data; Data Set; Disease; Environmental Exposure; Frequencies; Gene Cluster; Gene Frequency; Genes; Genetic; Goals; Growth; Individual; Mitochondria; Modeling; Mutation; Nuclear; Nucleic Acid Regulatory Sequences; Odds Ratio; 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）的遗传学研究一直是推动巨大的 研究的增长。然而，越来越多的人认识到，仅仅是常见的变化（MAF > 5%）， 不负责遗传贡献的风险发展为PD和许多其他复杂的疾病。 这种缺失的遗传贡献的替代假设之一是罕见的变异。一年来 我们启动了帕金森病的第一个全外显子组测序（WES）项目， 罕见变异导致PD。这个项目继续这项工作，结合了我们最近的工作， 我们的分析，并将提供信息的途径和功能的基因发现。 特定目标1在500个发现集中鉴定出初始的一组罕见变异和额外的SNP。 帕金森病患者和500名对照在Specific Aim 3a的复制数据集中进行测试。 Specific Aim 2利用一个庞大的Amish血统，使用WES，靶向捕获和 潜在的全基因组测序。阿米什人是一群既有相对 统一的环境暴露史和增加的遗传同质性。连锁分析显示， 在系谱的几个分支中，9号染色体上的强基因座，以及其他分支上的附加基因座。 染色体因此，这是远系繁殖群体中PD的良好模型。在第三章中，我们将测试 在另外500个病例和500个对照中，我们发现数据集中的前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靶向捕获。分析 该验证数据集将包括多个数据子集，包括基因内的变体 “聚类”、途径分析、感兴趣的基因网络，如线粒体核基因和AAO 差异为了改善途径的信息，并评估已鉴定的基因， 与其他已知的PD基因的关系，我们将使用沉默和其他方法研究差异表达。 通过核心D在三种不同生物系统中的候选基因的干预技术： 酵母、斑马鱼和来自PD患者和对照的诱导多能干细胞。