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

 描述（由申请人提供） 帕金森氏病（PD）是一种以静止性震颤、运动迟缓、肌肉强直和姿势不稳定为特征的黑质的成人发作的神经退行性疾病，并且代表神经退行性疾病的第二最常见原因。不幸的是，据估计，迄今为止，只有约30-40%的家族性PD的潜在遗传原因得到了解释。孟德尔遗传病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（R56 NS 082349）的一部分，我们目前正在遗传疾病研究中心（CIDR）对1，567例家族性PD病例进行外显子组测序。这些PD患者来自1，089个家族性PD家系，包括来自440个家系的多个PD病例。我们提出了一系列的目标，将利用从这些外显子组获得的信息，以确定新的基因有助于PD，然后探索通过功能研究确定的基因/变体的功能效果。本提案的具体目标是：（1）家族性PD相关新基因的发现我们将采用两种互补的方法来鉴定与家族性PD相关的新基因。（方法#1）将基于若干标准过滤所识别的变体以生成候选变体的缩小的集合。在多个家族中观察到的候选变异/基因将被给予最高优先级。（方法#2）通过与来自几个来源的超过20，000个对照样品的原始数据进行比较，将索引PD病例的外显子组进行无偏倚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中进行验证和表征。(2)与家族性PD相关的新基因的验证/表征。将在超过800个家族性PD和约5，000个对照外显子组的独立复制队列中验证来自目标#1的顶级候选基因。将排除未正确分离或在对照中以显著百分比存在的变体，并重新评价候选基因。我们的候选基因的更广泛的重要性将在超过3,000个散发性PD外显子组的队列中进行测试。基因将根据几个标准进行优先排序，包括变异的功能影响 鉴定、变异等位基因频率和eQTL以及剪接分析。(3)家族性PD相关新基因的功能分析将通过使用几种模型系统来评估鉴定的突变的功能后果。将使用已建立的测定法研究突变在诱导多能干细胞、果蝇和酵母模型中的致病作用。这些研究可能会发现与PD发展直接相关的其他基因和途径。我们相信，该项目将导致发现一个或多个与PD相关的新基因。这些基因的鉴定将导致对导致这种毁灭性疾病的缺陷的更多了解，并为PD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.