Identification of genes causative for familial ALS gene using exome sequencing

使用外显子组测序鉴定导致家族性 ALS 基因的基因

• 批准号: 8296297
• 负责人: JOHN E LANDERS
• 金额: $ 35.98万
• 依托单位: UNIV OF MASSACHUSETTS MED SCH WORCESTER
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-15 至 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8296297
• 关键词: Adopted; Adult; Affect; Amyotrophic Lateral Sclerosis; Bioinformatics; Candidate Disease Gene; DNA Sequence; Data; Defect; Development; Diagnostic; Disease; Exons; Familial Amyotrophic Lateral Sclerosis; Family; Genes; Genetic; Genome; Genotype; Knowledge; Lead; Longevity; Motor Neurons; Mutation; Nature; Neurodegenerative Disorders; Open Reading Frames; Pathogenesis; Pathway interactions; Patients; Population Control; Publishing; Reading; Sampling; Screening procedure; Series; Solutions; Technology; Variant; cohort; cost; exome; genetic pedigree; genome-wide; late disease onset; member; motor neuron degeneration; novel

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.

描述（由申请人提供）：肌萎缩侧索硬化症（ALS）是一种成人发病、进展迅速并最终致命的神经退行性疾病，由运动神经元的选择性丧失引起。尽管大多数 ALS 病例是散发性 (SALS)，但约 10% 是家族性 (FALS)。迄今为止，仅约 35% 的 FALS 病例找到了根本原因：20% 是由 SOD1 突变引起的，5% 是由 TARDBP 突变引起的，5% 是由 FUS 突变引起的。在其他家族中也发现了其他几个基因的变异，但程度较轻。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变性的细胞途径的了解。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变异在经济上还不可行。然而，自动化、短读长 DNA 测序的最新进展为这个问题提供了新的解决方案：现在可以仅对基因组的蛋白质编码区域（外显子组）进行测序，以降低成本，同时丰富发现高渗透性变异。该提案的目的是使用外显子组捕获和短读长测序的方法来识别 FALS 的新致病基因。该提案的具体目标是： (1) 对选定样本进行外显子捕获和短读长测序，以识别候选 FALS 特异性变体。将对 10 个 ALS 患病家庭 (20 FALS) 的 2 名远亲受影响成员进行外显子组捕获和短读长测序。然后，将使用一系列生物信息学过滤步骤创建导致 ALS 的候选变异的主要列表。 (2) 鉴定源自外显子组测序的 FALS 特异性变异。将通过对约 1,100 个对照样本组以及约 200 个 FALS 的附加组进行基因分型来询问候选变体。在 FALS 中检测到的变异，但在对照人群中未检测到的变异，高度提示存在致病性变化。 (3) 确定候选 FALS 基因是否在其他 FALS 家族中显示出不同的突变。将对约 200 个 FALS 样本中含有 FALS 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 FALS 中存在多个改变的基因将被视为因果关系。我们提出的研究将确定其突变导致 FALS 的新候选基因。从长远来看，了解 ALS 的遗传原因将有助于我们了解所有形式的 ALS，并协助开发诊断和治疗方法以延长 ALS 患者的寿命。