Full Human Genome Sequencing in ALS

描述(由申请人提供)：大多数神经退行性疾病(肌萎缩侧索硬化症、阿尔茨海默病和帕金森病)的原因尚不清楚，尽管在描绘这些疾病的罕见形式的分子病理学方面取得了显著进展，这些疾病作为孟德尔特征传播。拟议的项目将开发一个全基因组测序平台，以确定这些疾病的散发性和家族性形式及其发病机制背后的罕见遗传变异。这个项目专注于ALS，因为这种疾病的可怕性质，并且因为它可能在不同的神经退行性疾病中神经死亡机制重叠；对ALS发病机制的洞察将促进对其他疾病的研究。这一建议的中心假设是，识别易患ALS或改变这种疾病表型的自然发生的基因变异将识别作为新治疗策略开发目标的致病途径。这项建议是由两个实验室共同努力的，两个实验室在ALS和人类遗传学方面具有互补和协同的专业知识。罗伯特·布朗博士(麻省大学医学院神经病学专业)的实验室在肌萎缩侧索硬化症的遗传学方面有着长期的专长。与合作者一起，它在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KIFAP3的变异是ALS患者生存的修饰因素。大卫·戈尔茨坦博士(杜克大学基因组科学与政策研究所所长)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。该实验室有进行大规模人类遗传学研究的可靠记录，并开发了一套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和其他神经退行性变生物学研究的范式转变。该项目有五个具体目标：(1)对40例肌萎缩侧索硬化症(ALS)患者(20例散发，20例家族性)的基因组进行全序列测定和基因变异的鉴定；(2)验证已确定的变异，并将其优先用于进一步研究；(3)在1,000例病例和1,000名对照的队列中对排序的变异进行基因分型，并进行关联和回归分析，以评估这些变异作为易感性和/或表型的决定因素；(4)对重要变异的功能意义进行后续研究；(5)公布完整的测序数据供公众使用。 公共卫生意义：肌萎缩侧索硬化症，也被称为ALS或Lou Gehrig病，是一种致命的运动神经退行性疾病，通常在不到五年的时间内导致虚弱和死亡。一些研究表明，遗传因素在这种疾病中很重要，对于10%的ALS家族性病例和另外90%的ALS病例来说，微妙的基因变异是导致运动神经死亡的过程之一。我们建议对40例肌萎缩侧索硬化症患者进行完整的DNA分子序列测定。这40个病例的结果将在1000名ALS患者和另外1000名非ALS患者的DNA中进行进一步测试。导致肌萎缩侧索硬化症或影响其进化方式的基因变异的发现，将为人们提供对这种毁灭性疾病的新见解，同时为新疗法的开发确定新的靶点。这项工作将由杜克大学大卫·戈尔茨坦博士领导的世界级人类遗传学实验室和马萨诸塞大学在ALS遗传学方面具有长期经验的实验室联合开展。这是一个及时的尖端项目，有可能成为ALS生物学研究的范式转变；我们预计，这项研究的发现将为阿尔茨海默氏症和帕金森氏症等其他神经退行性疾病提供洞察力。

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.