Identification of genes causative for familial ALS gene using exome sequencing

描述（由申请人提供）：肌萎缩侧索硬化症（ALS）是一种由运动神经元选择性丧失引起的成人发病、快速进展并最终致命的神经退行性疾病。虽然大多数ALS病例是散发性的（SALS），但约10%是家族性的（FALS）。迄今为止，仅在约35%的所有FALS病例中确定了根本原因：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其他家族中也被发现，但程度较低。遗传学研究为理解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变性的细胞途径的认识。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变异在经济上是不可行的。然而，最近在自动化、短读段DNA测序方面的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（外显子组）进行测序，以降低成本，同时丰富高渗透变体的发现。该建议的目的是使用外显子组捕获随后进行短读测序的方法来鉴定新的FALS致病基因。本提案的具体目的是：（1）对选定的样本进行外显子捕获和短读段测序，以鉴定候选CDS特异性变体。将对10个ALS患病家族（20个FALS）的2个远亲受影响成员进行外显子组捕获和短读段测序。然后将使用一系列生物信息学过滤步骤创建导致ALS的候选变体的主要列表。(2)鉴定源自外显子组测序的对FALS特异的变体。将通过对一组约1，100份对照样本以及另一组约200份FALS样本进行基因分型来询问候选变体。在FALS中检测到但在对照人群中未检测到的变异体高度提示致病性变化。(3)确定候选FALS基因是否在其他FALS家族中显示不同的突变。将在约200份FALS样本中对携带ALS特异性变体的候选基因进行测序，以识别其他变体。在对照群体中未观察到的具有FALS多重变异的基因将被认为是因果关系。我们提出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ALS的遗传原因将有助于我们了解各种形式的ALS，并有助于开发诊断和治疗方法，以延长ALS患者的寿命。 公共卫生相关性：肌萎缩侧索硬化症（ALS），也称为Lou Gehrig病，是一种由运动神经元选择性丧失引起的成人发病、快速进展并最终致命的神经退行性疾病。家族性ALS的潜在遗传原因仅在约35%的病例中被确定。该提案的目的是确定家族性ALS的新致病基因，这将有助于我们了解这些缺陷如何导致疾病，并有助于开发诊断和治疗方法，以延长患者的寿命。

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. PUBLIC HEALTH RELEVANCE: Amyotrophic lateral sclerosis (ALS), also known as Lou Gehrig's disease, is an adult-onset, rapidly progressive and ultimately fatal neurodegenerative disease caused by the selective loss of motor neurons. The underlying genetic cause of familial forms of ALS has been identified in only ~35% of cases. The purpose of this proposal is to identify novel causative genes for familial ALS which will facilitate our understanding how such defects lead to disease as well as assisting in the development of diagnostics and therapies to extend the lifespan of patients.