Analysis and characterization of a cohort of familial Parkinson's disease exomes

 描述(由申请人提供) 帕金森病是一种以静止性震颤、运动迟缓、肌肉僵硬和姿势不稳为特征的成人起病的黑质神经退行性疾病，是神经退行性疾病的第二大常见原因。不幸的是，到目前为止，估计只有30-40%的家族性帕金森病的潜在遗传原因得到了解释。孟德尔病的致病突变的鉴定对于我们理解其发病机制至关重要。作为NIH高优先级短期项目奖(R56NS082349)的一部分，我们目前正在遗传病研究中心(CIDR)对1,567例家族性PD病例进行外显子组测序。这些帕金森病患者来自1089个家族性帕金森病家系，包括来自440个家系的多个帕金森病患者。我们提出了一系列目标，旨在利用从这些外显子获得的信息来识别与帕金森病相关的新基因，然后探索通过功能研究确定的基因/变体的功能效应。这项建议的具体目标是：(1)家族性帕金森病相关新基因的发现我们将使用两种互补的方法来识别与家族性帕金森病相关的新基因。(方法1)将根据几个标准对已识别的变体进行筛选，以生成缩小的候选变体集。在多个家系中观察到的候选变异/基因将被给予最高优先考虑。(方法2)通过与来自几个来源的20,000多个对照样本的原始数据进行比较，将对索引PD病例的外显子进行无偏见的全基因组罕见变异分析。来自每种方法的前25个候选基因将在目标2中得到验证和表征。(2)与家族性帕金森病相关的新基因的验证/表征。来自AIM#1的顶级候选基因将在一个由800多个家族性PD和~5,000个对照外显子组成的独立复制队列中得到验证。没有正确分离或在对照中存在显着百分比的变异将被排除，并重新评估候选基因。我们的候选基因的更广泛的重要性将在3000多个零星的PD外显子队列中进行测试。基因的优先顺序将基于几个标准，包括变异的功能影响 鉴定、变异等位基因频率、eQTL和剪接分析。(3)家族性帕金森病相关新基因的功能分析。将通过使用几个模型系统来评估已识别的突变的功能后果。将使用已建立的检测方法研究诱导多能干细胞、果蝇和酵母模型中突变的致病作用。这些研究可能确定与帕金森病的发展直接相关的其他基因和途径。我们相信，拟议的项目将导致一个或多个与帕金森病相关的新基因的发现。这些基因的识别将增加对导致这种毁灭性疾病的缺陷的了解，并为帕金森病科学界开辟新的研究途径，以及开发新的治疗靶点。

 DESCRIPTION (provided by applicant) Parkinson's disease (PD) is an adult-onset neurodegenerative disease of the substantia nigra characterized by resting tremor, bradykinesia, muscular rigidity and postural instability and represents the second most common cause of neurodegenerative disease. Unfortunately, it is estimated that only ~30-40% of the underlying genetic causes of familial form of PD have been explained to date. The identification of causative mutations for Mendelian disorders is critical fo our understanding of their pathogenesis. As part of a NIH High Priority, Short-Term Project Award (R56NS082349), we are currently performing at the Center for Inherited Disease Research (CIDR) exome sequencing of 1,567 familial PD cases. These PD patients are from 1,089 familial PD pedigrees, including multiple PD cases from 440 pedigrees. We propose a series of aims that will leverage the information gained from these exomes to identify novel genes contributing to PD and then explore the functional effect of the genes/variants identified through functional studies. The Specific Aims of this proposal are: (1.) Discovery of Novel Genes Associated with Familial PD. We will employ two complementary approaches to identify novel genes associated with familial PD. (Approach #1) Identified variants will be filtered based on several criteria to generate a narrowed set of candidate variants. Candidate variants/genes observed in multiple families will be given highest priority. (Approach #2) The exomes of index PD cases will be subject to an unbiased genome-wide rare variant analysis by comparing to the raw data of over 20,000 control samples derived from several sources. The top 25 candidate genes from each approach will be validated and characterized in Aim #2. (2) Validation/Characterization of Novel Genes Associated with Familial PD. Top candidate genes from Aim #1 will be validated in an independent replication cohort of over 800 familial PD and ~5,000 control exomes. Variants that do not segregate properly or are present at a signification percentage in controls will be excluded and the candidate gene re-evaluated. The broader importance of our candidate genes will be tested in a cohort of over 3,000 sporadic PD exomes. Genes will be prioritized based on several criteria including the functional impact of the variants identified, variant allele frequencies and eQTL and splicing analysis. (3) Functional Analysis Novel Genes Associated with Familial PD. The functional consequences of identified mutations will be evaluated though the use of several model systems. The pathogenic effect of the mutations in induced pluripotent stem cells, Drosophila and yeast models will be studied using established assays. These studies may identify additional genes and pathways that have direct relevance to the development of PD. We are confident that the proposed project will lead to the discovery of one or more novel genes associated with PD. The identification of such genes will lead to an increased knowledge of the defects contributing to this devastating disease and open new avenues of research for the PD scientific community as well as the development of new therapeutic targets.