Identification and Characterization of ALS/FTD Associated Variants Using Whole Genome Sequencing

使用全基因组测序鉴定和表征 ALS/FTD 相关变异

基本信息

批准号：
10216070
负责人：
JOHN E LANDERS
金额：
$ 58.63万
依托单位：
UNIV OF MASSACHUSETTS MED SCH WORCESTER
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-07-15 至 2022-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10216070
关键词：
ALS patients Adult Algorithms Alleles Amyotrophic Lateral Sclerosis Axon Axonal Transport Biological Assay Code Communities Copy Number Polymorphism DNA Damage Data Databases Development Disease Disease model Elements Enhancers Etiology Frontotemporal Dementia Gene Expression Gene Expression Regulation Gene Frequency Gene Proteins Genetic Genetic study Genome Heterozygote Investigation Knowledge MicroRNAs Motor Neurons National Heart, Lung, and Blood Institute Nature Neurodegenerative Disorders Nucleotides Pathogenesis Patients Pattern Phase Play Predisposition Process RNA Splicing Research Resources Role Sampling Structure Symptoms Testing Trans-Omics for Precision Medicine Untranslated RNA Validation Variant base case control cell growth regulation cohort cost exome sequencing frontotemporal lobar dementia-amyotrophic lateral sclerosis genetic element genetic variant genome sequencing genome-wide human disease induced pluripotent stem cell insertion/deletion mutation mouse model new therapeutic target novel nucleocytoplasmic transport protein function rare variant screening serial imaging transcriptome whole genome

项目摘要

Project Summary/Abstract Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease caused by the selective loss of motor neurons. It is ultimately lethal with a typical patient survival of two to five years. Symptoms of frontotemporal dementia (FTD) can be detected in up to 50% of ALS patients and it is generally accepted the ALS and FTD represent a continuum of disease (ALS/FTD). Although the etiology of a vast majority of ALS/FTD cases is largely unknown, rare genetic factors likely play a major role in susceptibility to the disease. Until recently, genetic studies have utilized data derived from exome sequencing due to the prohibitive cost of whole genome sequencing (WGS) limiting analysis to coding regions of the genome. Variants within non- coding genetic elements have been increasingly shown to be of vital importance in cellular regulation and human disease. Such non-coding genetic elements include miRNAs, lncRNAs, and enhancers/silencers of gene expression. However, dramatic reductions in the cost of whole genome sequencing now allow for the screening of case:control cohorts for rare variants at a genome-wide scale. Furthermore, the identification of structural variants, such as copy number variants, insertions, deletions and large rearrangements are overcome through the use of WGS allowing for association studies for these elements with ALS/FTD. Through our own efforts and the contributions of collaborators, we have amassed raw WGS data from over 5,000 ALS/FTD cases. Further, this cohort is expected to double in size to over 10,000 ALS/FTD cases within the next 3 years. Here, we propose to identify and characterize novel genetic variants associated with ALS/FTD. The Specific Aims of this proposal are: (1) Discovery of Candidate Genetic Variants Associated with ALS/FTD. Raw WGS from our ALS/FTD cohort will be combined with raw WGS data generated from the NHLBI’s TOPMed project representing up to 120,000 controls. After QC, variants (single nucleotide, indels and other structural variants) will be identified and subject to numerous case:control analyses to identify novel candidate variants associated with ALS/FTD. (2) Validation / Characterization of Novel Variants Associated with ALS/FTD. Top candidate genetic variants will be replicated in an independent replication cohort of an additional ~10,000 ALS/FTD cases through the Project MinE consortium. Validated elements will be evaluated by several algorithms/databases to predict their potential functional impact and prioritized based on their predicted functional impact to determine those that will be subject to functional analyses. (3) Functional Analysis of Novel Variants Associated with ALS/FTD. Variants associated with ALS/FTD will be evaluated in isogenic iPSC-derived motor neurons (iMNs) and murine models through several functional analyses. These include survival/axon outgrowth by longitudinal imaging, axonal transport, nuclearcytoplasmic transport, DNA damage, and global gene expression/splicing patterns. These studies will further our understanding of the impact of the variant towards ALS/FTD pathogenesis.

项目概要/摘要肌萎缩侧索硬化症（ALS）是一种成人发病的神经退行性疾病，由选择性丧失引起它最终是致命的，典型的患者生存期为两到五年。高达 50% 的 ALS 患者可检测到额颞叶痴呆 (FTD)，人们普遍认为 ALS 和 FTD 代表了疾病的连续体（ALS/FTD），尽管绝大多数的病因是这样的。 ALS/FTD 病例很大程度上未知，罕见的遗传因素可能在该疾病的易感性中发挥重要作用。直到最近，由于成本高昂，遗传学研究一直利用外显子组测序的数据。全基因组测序 (WGS) 将分析限制在基因组内的编码区域。越来越多的证据表明编码遗传元件在细胞调节和此类非编码遗传元件包括 miRNA、lncRNA 和增强子/沉默子。然而，现在全基因组测序成本的大幅降低使得基因表达成为可能。在全基因组范围内筛选病例：对照队列中的罕见变异。结构变异，例如拷贝数变异、插入、缺失和大的重排通过使用 WGS 可以对这些元素与 ALS/FTD 进行关联研究来克服这一问题。在我们自己的努力和合作者的贡献下，我们收集了来自 5,000 多个的原始 WGS 数据此外，该群体的 ALS/FTD 病例数量预计将增加一倍，达到 10,000 多例。在此，我们建议识别和表征与 ALS/FTD 相关的新基因变异。该提案的具体目标是： (1) 发现与我们的 ALS/FTD 队列中的原始 WGS 将与从 ALS/FTD 生成的原始 WGS 数据相结合。 NHLBI 的 TOPMed 项目代表多达 120,000 个 QC 后的对照、变异（单核苷酸、插入缺失和缺失）。其他结构变体）将被识别并受到许多案例的影响：控制分析以识别新的与 ALS/FTD 相关的候选变体 (2) 新变体的验证/表征。与 ALS/FTD 相关的顶级候选基因变异将在独立复制中进行复制。通过 Project MinE 联盟验证的元素将增加约 10,000 个 ALS/FTD 病例。通过多种算法/数据库进行评估，以预测其潜在的功能影响并根据优先级进行排序根据其预测的功能影响来确定将进行功能分析的内容 (3)。与 ALS/FTD 相关的新变异体的功能分析与 ALS/FTD 相关的变异体将是通过多种功能在同基因 iPSC 衍生的运动神经元 (iMN) 和小鼠模型中进行评估这些包括通过纵向成像、轴突运输、核细胞质的存活/轴突生长。这些研究将进一步推动我们的研究。了解该变异对 ALS/FTD 发病机制的影响。