Gene Dosage Imbalance in Neurodevelopmental Disorders

描述(由申请人提供)：越来越多的证据表明，亚显微基因组失衡(缺失、重复)在人类疾病中发挥着重要作用，特别是精神发育迟缓和自闭症等神经发育障碍。我们建议检验这一假设，即人类基因组的亚端粒和着丝粒周围区域由于其独特的基因组拓扑结构，非常容易发生基因组不稳定，并导致不成比例的发育障碍。它们复杂的马赛克结构富含重复和复制的序列，这一直是全基因组测序努力的顽固不化。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。我们提出了以下具体目标：1)研究人类亚端粒和着丝粒周围区域的基因组结构。我们将为每个亚端粒和着丝粒周围区域建立唯一和重复的DNA区之间的边界，并从每个端粒或着丝粒创建长达5Mb的“分子尺子”。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)确定亚端粒和着丝粒周围区域染色体异常的频率、模式和机制。涉及端粒以下或着丝粒周围区域的异常患者将使用我们的新型分子标尺试剂进行FISH和/或阵列CGH分析。基因剂量效应将在a)MR或自闭症患者和b)亚端粒或着丝粒不平衡的表型正常个体中进行评估。3)利用两种方法编制人类染色体着丝粒周围和亚端粒区域的“人类基因剂量图”：a)对精确校准的剂量不平衡片段内的基因含量进行计算研究，作为研究人类基因型-表型相关的高分辨率方法；b)利用包含约33,000个基因的寡核苷酸阵列在全球范围内调查与基因组不平衡相关的基因表达变化的功能研究，然后使用RT-PCR和/或Northern分析进行有针对性的分析，以评估直接参与染色体事件的基因及其邻近基因的表达(位置效应)和全基因组调查(基因交互效应)。

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).