Comprehensive genomic approach to rare hearing disorders and ataxia

描述（由申请人提供）：位置克隆已经帮助确定了许多孟德尔疾病的分子原因。与更常见的耳聋和共济失调有关的基因已经被确定，并经常进行临床测试。然而，大多数遗传罕见形式的原因仍然未知，因为这些家庭往往太小，无法提供足够的统计力量来明确确定联系。此外，即使家族足够大，可以确定一个连锁位点，但这些区域通常太大，以至于涉及数百个基因。在某些情况下，链接不平衡分析可以进一步缩小区域。最近，基因表达的全球分析已经成为现实。我们假设，一部分突变基因直接或间接导致了异常的表达水平，并且可以通过结合遗传分析和来自淋巴母细胞样细胞系（LCLs） mRNA的基因表达分析来鉴定。利用这种综合方法，最近仅在三个受影响的受试者中发现了一种新的癫痫基因。我们最近发现了一种新的听神经病变基因，并在发现第二种新的耳聋基因和几种新的共济失调基因方面获得了令人鼓舞的数据。在这个试点/可行性R21拨款中，我们将探索这种方法在几个原因不明的耳聋或共济失调家庭中的普遍性。我们将进行遗传连锁，连锁不平衡和全局基因表达分析。候选基因将被识别为连锁区域基因和那些表现出显著表达变化的基因之间的截距。计算方法来定义遗传和基因表达数据之间的交集将被开发、实施和测试。在某些情况下，结合遗传连锁和连锁不平衡与全局基因表达分析可以直接识别突变基因，而在另一些情况下，突变可能导致一条通路的功能差异，而不直接影响其自身基因的表达。在这种情况下，有必要对突变基因下游受影响的基因表达变化进行更复杂的分析，以确定缺陷途径和突变。来自表达分析、动物模型、文献和公共生物信息学数据库的途径将用于此目的。从这些方法中产生的候选基因将被测序以确定变异，并在不相关的对照中测试潜在的突变。

DESCRIPTION (provided by applicant): Positional cloning has helped identify the molecular causes of many of Mendelian disorders. Genes involved in the more common forms of deafness and ataxia have been identified and are often clinically tested. However, the cause of most genetically rare forms is still unknown because such families are often too small to provide by themselves sufficient statistical power to unambiguously identify linkage. In addition, even if families are large enough to identify a linked locus, the regions are typically so large that hundreds of genes are implicated. In some situations, linkage disequilibrium analysis can further narrow a region. Recently, global analysis of gene expression has become a reality. We hypothesize that a subset of mutated genes directly or indirectly leads to abnormal expression levels, and can be identified by combining genetic analysis with gene expression analysis of mRNA from lymphoblastoid cell lines (LCLs). Using such a combined approach, a novel epilepsy gene was recently identified in only three affected subjects. We have recently identified a novel auditory neuropathy gene, and have encouraging data for identification of a second novel deafness gene and for several novel ataxia genes. In this pilot/feasibility R21 grant, we will explore the generalizability of this approach in several families with unidentified causes of deafness or ataxia. We will perform genetic linkage, linkage disequilibrium and global gene expression analysis. Candidates genes will be identified as the intercept between genes in linkage regions and those that show significant expression changes. Computational approaches to define the intersect between genetic and gene expression data will be developed, implemented and tested. While in some cases combining genetic linkage and linkage disequilibrium with global gene expression analysis may directly identify the mutant gene, in other cases the mutation may result in functional differences in a pathway without affecting the expression of its own gene directly. In that case, more complex analysis of affected gene expression changes downstream of a mutant gene will be necessary to identify the deficient pathway and the mutation. Pathways from expression analysis, animal models and the literature and public bioinformatic databases will be used for this purpose. Candidate genes emerging from these approaches will be sequenced to identify variants, and potential mutations tested in unrelated controls. PUBLIC HEALTH RELEVANCE: The genetic cause of many forms of deafness or ataxia is still unknown. Our research will result in the identification of new genes and metabolic pathways involved in these disorders. These findings can improve accurate diagnosis, presymptomatic testing, family planning and personalizing treatment. It may also ultimately lead to new treatments.