Full Human Genome Sequencing in ALS

描述（由申请人提供）：大多数神经退行性疾病（ALS，阿尔茨海默病和帕金森病）的病因尚不清楚，尽管在描述这些罕见形式的疾病的分子病理学方面取得了显著进展，这些疾病是作为孟德尔特征传播的。拟议的项目将开发一个全基因组测序平台，以确定罕见的遗传变异，这些变异是这些疾病的散发性和家族性形式及其发病机制的基础。该项目专注于ALS，因为这种疾病的可怕性质，因为神经死亡机制可能在多种神经退行性疾病中重叠；对ALS发病机制的深入了解将促进其他疾病的研究。该提案的中心假设是，鉴定易患ALS或修饰该疾病表型的自然发生的基因变异将确定作为开发新治疗策略目标的致病途径。该提案是两个在ALS和人类遗传学方面具有互补和协同专长的实验室的共同努力。罗伯特·布朗博士的实验室（PI，神经病学，马萨诸塞大学医学院）在ALS的遗传学方面有着长期的专业知识。与合作者在1993年报道了第一个ALS基因（SOD1），随后参与了其他ALS基因的报道，包括alsin， VAPB，以及最近的FIG4， ELP3和FUS。该小组领导了多国基因组分析，确定了KIFAP3的变异是ALS患者生存的修饰因子。David Goldstein博士（杜克大学基因组科学与政策研究所联合主任）的实验室是进行大规模全基因组测序的最重要的学术设施之一。该实验室在进行大规模人类遗传学研究方面有良好的记录，并开发了生物信息学和生物统计学管道，用于分析全基因组测序产生的大量数据。在我们看来，这是一次及时的、前沿的合作，有可能成为ALS和其他神经退行性疾病生物学研究的范式转变。该项目有五个具体目标：(1)对40例ALS患者（20例散发性，20例家族性）进行全基因组测序和基因变异鉴定；(2)对识别出的变异进行验证，并对其进行优先排序，以供进一步研究；(3)对1000例病例和1000例对照进行基因分型，并进行关联和回归分析，以评估这些变异是否为易感性和/或表型的决定因素；(4)对显著变异的功能意义进行后续研究；(5)公布全部测序数据供公众使用。

DESCRIPTION (provided by applicant): The causes of most neurodegenerative disorders (ALS, Alzheimer and Parkinson disease) are poorly understood, despite remarkable advances in delineating the molecular pathology in the rare forms of these diseases that are transmitted as Mendelian traits. The proposed project will develop a platform for full genome sequencing that will identify rare genetic variants that underlie both sporadic and familial forms of these disorders their pathogenesis. This project focuses on ALS because of the dire nature of this disease and because it is likely that neural death mechanisms overlap in diverse neurodegenerative disorders; insights into the pathogenesis in ALS will facilitate research in the others. The central hypothesis of this proposal is that the identification of naturally occurring gene variants that predispose to ALS or that modify the phenotype of this disease will identify pathogenic pathways that are targets for the development of new therapeutic strategies. This proposal is a joint effort of two laboratories with complementary and synergistic expertise in ALS and human genetics. The laboratory of Dr. Robert Brown (PI, Neurology, University of Massachusetts Medical School) has a longstanding expertise in the genetics of ALS. With collaborators, it reported the first ALS gene (SOD1) in 1993 and subsequently participated in reports of additional ALS genes including alsin, VAPB, and most recently FIG4, ELP3 and FUS. This group led the multinational genome analysis that identified variants in KIFAP3 as modifiers of survival in ALS. The laboratory of Dr. David Goldstein (Co-PI, Director, The Institute for Genome Science and Policy, Duke University) is among the foremost academic facilities conducting whole-genome sequencing on a significant scale. The laboratory has a proven track record of performing large-scale human genetics studies, and has developed a bioinformatics and biostatistical pipeline for the analysis of the large amounts of data arising from whole-genome sequencing. In our view, this is a timely, cutting edge collaboration that has the potential to be a paradigm shift in studies of the biology of ALS and other neurodegenerative. The project has five specific aims: (1) perform full sequencing of the genome and identification of the genetic variants in 40 ALS cases (20 sporadic, 20 familial); (2) validate the identified variants and prioritize them for further study; (3) genotype the ranked variants in cohorts of 1,000 cases and 1,000 controls and perform association and regression analyses to assess these variants as determinants of susceptibility and/or phenotype; (4) undertake follow-up studies of the functional significance of the significant variants; (5) release the full sequencing data for public use. PUBLIC HEALTH RELEVANCE: Amyotrophic lateral sclerosis, also called ALS or Lou Gehrig's disease, is a lethal degenerative disease of motor nerves that causes weakness and death, usually in less than five years. Several studies suggest that genetic factors are important in this disease, both for the 10% of cases in which ALS runs in families and for the other 90%, in which subtle gene variations are contribute to the process of motor nerve death. We propose to completely determine the sequences of all of the molecules of DNA in a each of 40 individuals with ALS. The findings in these 40 cases will then be further tested in DNA from 1,000 individuals with ALS cases and another 1,000 individuals who do not have ALS. The discovery of gene variants that cause ALS, or that affect the way it evolves, will provide new insight into this devastating disease and, at the same time, identify novel targets for the development of new therapies. This work will be undertaken jointly by a world-class human genetics laboratory directed by Dr. David Goldstein at Duke University and by a laboratory with longstanding experience in ALS genetics at the University of Massachusetts. This is a timely, cutting edge project that has the potential to be a paradigm shift in studies of the biology of ALS; we anticipate that findings from this study will provide insight into other neurodegenerative disorders such as Alzheimer's and Parkinson's diseases.