De novo copy number variation and gene discovery in human brain malformations

描述(申请人提供)：在过去的几十年里，被确认的脑畸形和综合征的数量迅速增加，但确定的致病基因相对较少，尤其是三种常见的畸形，这三种畸形与大量细胞遗传学上可见的染色体缺失和重复有关，并且经常同时发生：胼胝体发育不全(ACC)、包括Dandy-Walker畸形(DWM)在内的小脑蛔虫发育不良(CVH)和多小脑回(PMG)。我们建议进行高分辨率阵列比较基因组杂交(ACGH)，这是一种新兴的技术，能够检测到小拷贝数变异(CNV)，在700名患有这三种畸形中的一种或多种的先证者中。我们的中心假设是，超过10%的ACC、CVH或PMG患者的新生CNV低于常规细胞遗传学分析的分辨率，但可被当前的阵列平台检测到。因此，我们希望确定70-100名小CNV患者。我们将区分在正常个体中发现的CNV与潜在的疾病相关变化，并将使用荧光原位杂交(FISH)和微卫星(STRP)分析来确认CNV。我们将优先考虑新生的、涉及2个或更多BAC的CNV，其次是家族性和较小的CNV，排除已知的基因多态。之后，我们将使用公共数据库中的信息和我们自己的表达研究来评估和排序关键区域中的候选基因，并通过对大量表型与CNV定义关键区域的患者的表型匹配的受试者进行测序，对定义明确的关键区域中的最佳候选基因进行突变分析。在这里，我们将使用更精细的标准来补充我们的临床分类，例如发育水平和癫痫或其他出生缺陷的存在。任何发现的异常都将使用关于多态(即，DBSNP)、跨物种比较和适用于特定序列变化的功能分析的现有数据进行分析。我们希望我们对小染色体不平衡的关注能有效地导致发现导致这三种焦点畸形的新基因。这些发现将直接导致改善对受影响儿童和家庭的护理，包括更准确的诊断和结果咨询，其中将包括具体的诊断测试，以及改进的遗传咨询。相关性：这项拨款中提议的工作将导致发现许多导致大脑出生缺陷和相关但往往不那么严重的发育障碍的基因。这些结果将立即被证明有助于向受影响儿童的家庭提供关于诊断和预后的更好信息，还将有助于更好地了解潜在的生物学，在某些情况下还将导致更有效的治疗。

DESCRIPTION (provided by applicant): The number of recognized brain malformations and syndromes has grown rapidly during the past several decades, yet relatively few causative genes have been identified, especially for three common malformations that have been associated with numerous cytogenetically visible chromosome deletions and duplications, and that often occur together: agenesis of the corpus callosum (ACC), cerebellar vermis hypoplasia (CVH) including Dandy-Walker malformation (DWM), and polymicrogyria (PMG). We propose to perform high-resolution array comparative genome hybridization (aCGH), emerging technology able to detect small copy number variants (CNV), in 700 probands with one or more of these three malformations. Our central hypothesis states that more than 10% of patients with ACC, CVH or PMG will have de novo CNV below the resolution of routine cytogenetic analysis, but detectable by current array platforms. We therefore expect to identify 70-100 patients with small CNV. We will distinguish CNV found in normal individuals from potentially disease-associated changes, and will confirm CNV using fluorescence in situ hybridization (FISH) and microsatellite (STRP) analysis. We will give highest priority to CNV that are de novo and involve 2 or more BACs, and secondary priority to familial and smaller CNV excluding known polymorphisms. After that, we will evaluate and rank candidate genes in the critical regions using information from public databases and our own expression studies, and perform mutation analysis of the best candidate genes from well-defined critical regions by sequencing in a large panel of subjects with phenotypes that match the phenotypes of the patients whose CNV define the critical regions. Here, we will use more refined criteria to supplement our clinical classification, such as the developmental level and presence of epilepsy or other birth defects. Any abnormalities found will be analyzed using existing data regarding polymorphisms (i.e. dbSNP), cross-species comparisons, and functional assays appropriate for the specific sequence change. We expect our focus on small chromosome imbalances to efficiently lead to discovery of new genes that cause these three focus malformations. These discoveries will lead directly to improved care for affected children and families consisting of more accurate diagnosis and outcome counseling, which will include specific diagnostic testing, as well as improved genetic counseling. Relevance: The work proposed in this grant will lead to lead to the discovery of many of the genes that cause of birth defects of the brain and related - but often less severe - developmental disorders. These results will prove immediately helpful in providing better information regarding diagnosis and prognosis to the families of affected children, and will also lead to better understanding of the underlying biology and in some cases to more effective treatment.