Identification of genes causative for familial ALS gene using exome sequencing

描述(申请人提供)：肌萎缩侧索硬化症(ALS)是一种成人起病，进展迅速，最终致命的神经退行性疾病，由运动神经元选择性丧失引起。虽然大多数ALS病例是散发性的(SALS)，但约10%是家族性的(FAL)。到目前为止，仅有约35%的FALS病例确定了潜在原因：20%由SOD1突变引起，5%由TARDBP突变引起，5%由FUS突变引起。其他几个基因的变异在更多的家族中也被发现，程度较轻。遗传学研究为了解FALS和SALS的发病机制提供了宝贵的信息。毫无疑问，新的FALS相关基因的发现将极大地加深我们对导致运动神经元退化的细胞通路的了解。到目前为止，在受疾病影响的样本中在全基因组范围内筛选罕见的变异在经济上是不可行的。然而，自动化短读DNA测序的最新进展为这个问题提供了新的解决方案：现在可以只对基因组的蛋白质编码区(外显体)进行测序，以降低成本，同时丰富发现高渗透性变异的能力。这项建议的目的是利用外显子捕获和短读测序的方法识别FALS的新致病基因。这项建议的具体目标是：(1)对选定的样本进行外显子捕获和短读测序，以确定候选的FALS特异性变体。对10个肌萎缩侧索硬化症家系(20个家系)的2名远亲成员进行外显子组捕获和短读测序。然后将使用一系列生物信息过滤步骤创建导致ALS的候选变异的主要列表。(2)从外显子组测序中找出FALS特异的变异体。候选变异将通过对大约1,100个对照样本以及大约200个FAL的额外小组进行基因分型来询问。在FAL中检测到的变异，但不在对照人群中，高度暗示有致病变化。(3)确定候选FALS基因在其他FALS家系中是否表现出不同的突变。含有FALS特定变种的候选基因将在约200个FALS样本中进行测序，以确定其他变种。在对照人群中没有观察到的FAL中有多个变化的基因将被认为是因果关系。我们建议的研究将确定新的候选基因，其突变导致FALS。从长远来看，了解肌萎缩侧索硬化症的遗传原因将有助于我们了解各种形式的肌萎缩侧索硬化症，并有助于开发诊断和治疗方法来延长肌萎缩侧索硬化症患者的寿命。

DESCRIPTION (provided by applicant): Amyotrophic lateral sclerosis (ALS) is an adult-onset, rapidly progressive and ultimately fatal neurodegenerative disease caused by the selective loss of motor neurons. Although most ALS cases are sporadic (SALS), ~10% are familial (FALS). To date, the underlying cause has been identified in only ~35% of all FALS cases: 20% are caused by mutations in SOD1, 5% in TARDBP and 5% in FUS. Variants in several other genes have been found in additional families to a lesser degree. Genetic studies have provided invaluable information for understanding of the pathogenesis of both FALS and SALS. Undoubtedly, the discovery of novel FALS- associated genes will dramatically further our knowledge of the cellular pathways that lead to motor neuron degeneration. Until now, it was not economically feasible to screen for rare variants at a genome-wide scale within disease-affected samples. However, the recent advances in automated, short-read DNA sequencing offer new solutions to this problem: it is now possible to sequence only protein-coding regions of the genome (exomes) to reduce costs while enriching for the discovery of highly penetrant variants. The purpose of this proposal is to identify novel causative genes for FALS using the approach of exome capture followed by short- read sequencing. The Specific Aims of this proposal are to: (1) Perform exon capture and short-read sequencing of selected samples to identify candidate FALS-specific variants. Exome capture and short-read sequencing will be performed for 2 distantly-related affected members of 10 ALS afflicted families (20 FALS). A primary list of candidate variants causative for ALS will then be created using a series of bioinformatic filtering steps. (2) Identify the variants derived from exome sequencing that are specific for FALS. Candidate variants will be interrogated by genotyping a panel of ~1,100 control samples as well as an additional panel of ~200 FALS. Variants detected in FALS, but not within the control population, are highly suggestive of a causative change. (3) Determine if candidate FALS genes show different mutations in additional FALS families. Candidate genes harboring FALS-specific variants will be sequenced in ~200 FALS samples to identify additional variants. Genes with multiple alterations in FALS not observed in control populations will be considered causal. Our proposed studies will identify novel candidate genes whose mutations cause FALS. In the long term, understanding the genetic causes of ALS will facilitate our understanding of all forms of ALS as well as assisting in the development of diagnostics and therapies to extend the lifespan of ALS patients.