Ataxia gene identification by integrated genomic analysis

通过整合基因组分析鉴定共济失调基因

• 批准号: 8606519
• 负责人: Margit Burmeister
• 金额: $ 51.33万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-03-01 至 2016-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8606519
• 关键词: Affect; Ataxia; Auditory; Base Sequence; Bioinformatics; Biological Assay; Biopsy; Candidate Disease Gene; Cells; Code; Commit; Data; Data Set; Defect; Development; Diagnosis; Disease; Drug Targeting; Electrophysiology (science); Etiology; Family; Family Planning; Family member; Fibroblasts; Friedreich Ataxia; Future; Gene Expression Profiling; Gene Mutation; Genes; Genetic; Genetic screening method; Genome; Genomics; Genotype; Haplotypes; Hereditary Disease; Human; Individual; Inherited; Inherited Spinocerebellar Degenerations; Knowledge; Lead; Lesion; Linkage Disequilibrium; Maps; Massive Parallel Sequencing; Messenger RNA; Modeling; Molecular; Mutation; Myopathy; Neurons; Neuropathy; Nuclear; Pathway Analysis; Pathway interactions; Patients; Persons; Phenotype; Protein Binding; RNA Splicing; Recruitment Activity; Reporter; Reverse Transcriptase Polymerase Chain Reaction; Sampling; Techniques; Technology; Testing; Variant; base; cell type; clinical care; clinical practice; congenital myopathy; deafness; drug development; exome; experience; follow-up; gene discovery; genetic linkage; genetic linkage analysis; genetic pedigree; genome sequencing; in vitro Assay; induced pluripotent stem cell; lymphoblastoid cell line; member; nervous system disorder; next generation sequencing; novel; outcome forecast; positional cloning; tool

DESCRIPTION (provided by applicant): Ataxias are a heterogeneous group of neurological disorders caused by environmental as well as genetic factors. While mutations in more than 40 genes have been implicated in hereditary ataxia, and genetic testing has become an increasingly routine clinical practice, most sporadic and many inherited cases are still of unknown origin. Individual families with unexplained ataxia are often too small to allow gene identification by traditional positional cloning approaches; and the lack of understanding of ataxia etiology in these cases continues to hamper accurate diagnosis and identification of novel targets for effective and personalized therapy. Recently, massively parallel sequencing allows efficient discovery of nearly all variants in a genome, or at least its coding portion. However, as each person carries thousands of novel variants, sequencing alone does not permit immediate identification of causative mutations. Here, we hypothesize that genetic linkage, sequencing-based variant discovery, and gene expression analysis, while not sufficiently informative separately, provide complementary information and allow identification of novel ataxia genes in families with a minimum of two recessive or three dominantly affected members. We already have recruited and started to analyze 12 such pedigrees, and have developed expertise to collect and analyze the relevant genomic data. We propose to study 22 pedigrees using an integrated pipeline that combines linkage analysis, gene expression profiling, next-generation sequencing, and gene network analysis. Since different ataxia families likely carry distinct variants, none of these techniques alone will be sufficient, but their combination will be highly informative to pinpoint candidates. Candidate mutations will be tested for absence in control samples, and candidate genes will be screened for additional mutations in unrelated cases. By using such an integrated approach we have recently identified an auditory neuropathy gene and have found a credible novel candidate gene for dominant central nuclear myopathy. We also have promising preliminary data for several ataxia pedigrees. In addition to global analyses of complementary genomic datasets, we are committed to rapid functional follow-up using appropriate neuronal cells. This is achieved by reprogramming fibroblasts from biopsy cultures from selected families into neurons, and testing the effect of potential mutations on splicing and amount of mRNA, on other genes within the relevant cell type, and on cellular phenotypes. We predict that this pipeline will lead to the identification of new rare ataxia gene mutations that were not previously possible using purely genetic positional cloning strategies. The discoveries will enable better diagnosis and prognosis which will immediately help the affected families. It may lead to personalized treatment & generate new hypotheses to study the more common sporadic forms of ataxia. The identification of validated & functionally characterized molecular lesions is expected to facilitat informed drug development. Our experience with this approach will also establish a useful paradigm for other rare Mendelian disorders.

描述（由申请人提供）： 共济失调是由环境和遗传因素引起的一群神经系统疾病的异质。尽管40多个基因的突变与遗传性共济失调有关，而基因检测已成为一种日益常规的临床实践，但大多数零星和许多遗传病例仍然是未知的起源。具有无法解释的共济失调的个体家庭通常太小，无法通过传统的位置克隆方法识别基因。在这些情况下，对共济失调病因的缺乏了解继续阻碍准确的诊断和确定有效和个性化治疗的新靶标。最近，大规模并行测序可以有效发现基因组中几乎所有变体，或者至少其编码部分。但是，由于每个人都携带了数千种新型变体，因此单独的测序不允许立即识别因果突变。在这里，我们假设遗传联系，基于测序的变体发现和基因表达分析，虽然没有足够的信息分别提供信息，但提供了互补的信息，并允许鉴定有两个隐性或三个受影响成员的家族中新型的共济失调基因。我们已经招募并开始分析12种此类谱系，并开发了专业知识来收集和分析相关的基因组数据。我们建议使用结合链接分析，基因表达分析，下一代测序和基因网络分析的集成管道来研究22个血统。由于不同的共济失调家族可能具有不同的变体，因此仅这些技术就足够了，但是它们的组合将非常有用，以指出候选人。候选突变将在对照样品中测试是否存在，并将在无关的情况下筛选候选基因以进行其他突变。通过使用这种综合方法，我们最近确定了一个听觉神经病基因，并发现了一个可靠的新型候选基因，用于主要的中央核肌病。我们还拥有多种共济失调的有希望的初步数据。除了对互补基因组数据集的全球分析外，我们还致力于使用适当的神经元细胞快速进行功能随访。这是通过从选定家族的活检培养物中重编程的成纤维细胞来实现的，并测试了潜在突变对剪接和mRNA剪接和量，对相关细胞类型中其他基因的剪接和量的影响以及细胞表型。我们预测，该管道将导致鉴定新的稀有共济失调基因突变，这些基因突变以前是使用纯粹的遗传位置克隆策略而言是不可能的。这些发现将实现更好的诊断和预后，这将立即帮助受影响的家庭。它可能导致个性化治疗并产生新的假设，以研究共济的零星形式。鉴定经过验证和功能表征的分子病变有望促进药物开发。我们在这种方法方面的经验还将为其他罕见的门德尔疾病建立有用的范例。