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

摘要 已确认的脑畸形和综合征的数量迅速增长 在过去的几十年里，已经鉴定出的致病基因相对较少， 特别是三种常见的畸形， 细胞遗传学上可见的染色体缺失和重复， 一起：胼胝体发育不全（ACC），小脑蚓部发育不全（CVH） 包括Dandy-Walker畸形（DWM）和多小脑回（PMG）。我们提出 进行高分辨率阵列比较基因组杂交（aCGH）， 一种能够检测小拷贝数变异（CNV）的技术，在700名先证者中， 或以上的畸形我们的核心假设是， 的ACC、CVH或PMG患者的新发CNV分辨率低于 常规细胞遗传学分析，但可通过当前阵列平台检测。因此我们 预计将发现70-100例小CNV患者。我们将区分CNV， 正常个体的潜在疾病相关变化，并将确认CNV 使用荧光原位杂交（FISH）和微卫星（STRP）分析。我们 将最优先考虑新发并涉及2个或更多BAC的CNV，以及 其次优先考虑家族性和较小的CNV，排除已知的多态性。后 即，我们将使用信息评估和排序关键区域中的候选基因， 从公共数据库和我们自己的表达研究，并进行突变分析， 通过大规模测序，从定义明确的关键区域中筛选出最佳候选基因， 表型与CNV患者表型匹配的受试者组 定义关键区域。在这里，我们将使用更精确的标准来补充我们的 临床分类，如癫痫或其他疾病的发展水平和存在 出生缺陷将使用现有数据分析发现的任何异常， 多态性（即dbSNP）、跨物种比较和功能测定 适合于特定的序列变化。 我们希望我们对小染色体不平衡的关注能有效地导致 发现导致这三种病灶畸形的新基因。这些发现 将直接改善对受影响儿童和家庭的照顾， 准确的诊断和结果咨询，其中将包括具体的诊断 测试，以及改善遗传咨询。相关性 这项工作将导致发现许多导致出生的基因 大脑缺陷和相关的--但通常不太严重的--发育障碍。这些结果将证明 立即有助于为受影响的家庭提供有关诊断和预后的更好信息 儿童，也将导致更好地了解潜在的生物学，在某些情况下， 有效治疗。

ABSTRACT 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.