Gene Dosage Imbalance in Neurodevelopmental Disorders

描述（由申请人提供）：越来越多的证据表明，亚微观基因组不平衡（缺失、重复）在人类疾病中起主要作用，特别是神经发育障碍，如精神发育迟滞和自闭症。我们建议测试的假设，即人类基因组的亚端粒和近着丝粒区域是非常容易基因组不稳定性，并导致不成比例的百分比发育障碍，由于其独特的基因组拓扑结构。它们复杂的镶嵌结构富含重复和重复的序列，这已经阻碍了全基因组测序的努力。需要有针对性的方法来阐明它们的基因组结构、进化和在人类疾病中的作用。我们提出以下具体目标：1）研究人类端粒下和着丝粒周围区域的基因组结构。我们将为每个亚端粒和近着丝粒区域建立独特和重复的DNA区域之间的边界，并从每个端粒或着丝粒创建高达5 Mb的“分子统治者”。将对每个区域进行分类（复杂与简单;多态与非多态），以检验复杂或多态结构可能增加不稳定性的假设。2)确定染色体异常的频率，模式和机制在亚端粒和近着丝粒区域。涉及亚端粒或近着丝粒区域异常的患者将使用我们的新型分子标尺试剂通过FISH和/或阵列CGH进行分析。将在a）MR或自闭症个体和B）具有亚端粒或近着丝粒失衡的表型正常个体中评估基因剂量效应。3)使用2种方法为人类染色体的近着丝粒和亚端粒区域开发“人类基因剂量图”：a）在精确校准的剂量不平衡片段内的基因含量的计算研究将被用作人类基因型-表型相关性的高分辨率方法，B）与基因组不平衡相关的基因表达变化的功能研究将使用~33，000个基因，然后使用RT-PCR和/或北方分析进行靶向分析，以评估直接参与染色体事件的基因以及邻近基因的表达（位置效应）和全基因组调查（基因相互作用效应）。

DESCRIPTION (provided by applicant): Increasing evidence indicates that submicroscopic genomic imbalances (deletions, duplications) play a major role in human disease, especially neurodevelopmental disorders such as mental retardation and autism. We propose to test the hypothesis that subtelomeric and pericentromeric regions of the human genome are highly prone to genomic instability and cause a disproportionate percentage of developmental disabilities due to their unique genomic topology. Their complex, mosaic structures are rich in repetitive and duplicated sequences, which have been recalcitrant to whole genome sequencing efforts. Targeted approaches are needed to elucidate their genomic architecture, evolution and role in human disease. We propose the following Specific Aims: 1) Investigate the genomic architecture of human subtelomeric and pericentromeric regions. We will establish the boundary between the unique and repetitive DNA zones for each subtelomeric and pericentromeric region and create "molecular rulers" up to 5 Mb from each telomere or centromere. Each region will be classified (complex vs. simple; polymorphic vs. non-polymorphic) to test the hypothesis that a complex or polymorphic structure may increase instability. 2) Determine the frequency, patterns and mechanisms of chromosome abnormalities at subtelomeric and pericentromeric regions. Patients with abnormalities involving subtelomeric or pericentromeric regions will be analyzed by FISH and/or array CGH using our novel molecular ruler reagents. Gene dosage effects will be assessed in a) MR or autistic individuals and b) phenotypically normal individuals with subtelomeric or pericentromeric imbalance. 3) Develop a "human gene dosage map" for the pericentromeric and subtelomeric regions of human chromosomes using 2 approaches: a) Computational studies of gene content within the precisely calibrated segments of dosage imbalance will be used as a high-resolution approach to genotype-phenotype correlation in humans, b) Functional studies of gene expression changes associated with genomic imbalance will be globally surveyed using oligonucleotide arrays of ~33,000 genes followed by targeted analyses using RT-PCR and/or northern analyses to assess expression of genes directly involved in the chromosomal event as well as neighboring genes (position effects) and a genome wide survey (gene interaction effects).