A novel method to resolve the complex genome rearrangements of the large copy number variants (CNVs) associated with psychiatric disorders

一种解决与精神疾病相关的大拷贝数变异（CNV）的复杂基因组重排的新方法

• 批准号: 10571847
• 负责人: Bo Zhou
• 金额: $ 17.94万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-15 至 2026-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10571847
• 关键词: 16p11.2; 1q21; 22q11; 22q11.2; Achievement; Affect; Base Pairing; Biological; Biological Assay; Biology; CRISPR/Cas technology; Career Mobility; Cell Line; Cells; Chromatin; Chromosome abnormality; Cicatrix; Clinical; Complex; Copy Number Polymorphism; DNA; DNA mapping; Development; Disease; Etiology; Functional disorder; Funding; Future; Gene Expression; Gene Expression Profile; Gene Fusion; Genetic; Genetic Polymorphism; Genetic Transcription; Genetic Variation; Genome; Genomic DNA; Genomic Segment; Genomics; Genotype; Goals; Grant; Haplotypes; Human; Individual; Knowledge; Mediating; Mental disorders; Mentorship; Methodology; Methods; Modeling; Molecular; Neurons; Neurosciences; Optics; Organoids; Outcome; Phenotype; Principal Investigator; Research; Research Personnel; Resolution; Risk Factors; Sampling; Schizophrenia; Secure; Stretching; Time; Training; Universities; Writing; autism spectrum disorder; career; career development; cell type; cohort; digital; established cell line; experience; functional outcomes; genome analysis; genome sequencing; homologous recombination; induced pluripotent stem cell; neural; neuropsychiatric disorder; neuropsychiatry; novel; novel strategies; paralogous gene; psychogenetics; research study; schizophrenia risk

Project Summary The proposed project serves as a platform to obtain the key training and research experiences in achieving the long-term career goal of becoming a leading academic principal investigator with a primary focus of developing and applying genomic methods to understand the complex genetic components and biological mechanisms of neuropsychiatric disorders. Chromosomal aberrations in the form of large deletions or duplications (copy number variants, CNVs), such as those on 1q21.1, 16p11.2, and 22q11.2, are the strongest known risk factors for neuropsychiatric disorders. For this reason, these large CNVs serve as key points of entry for investigating the molecular etiology. However, it is unknown why each of these CNVs is associated with diverse clinical outcomes. For example, deletions and duplications at 16p11.2 are strong risk factors for schizophrenia (SZ) and autism spectrum disorder (ASD). Duplications produce a greater than 10-fold increase in risk for SZ, but ASD is frequent in carriers of deletions as well as duplications. The large stretches of human-specific segmental duplications (HSDs) that both constitute and mediate the formation of these large “neuropsychiatric” CNVs are inaccessible to current genome sequencing analysis due to their high degree of repetitiveness and complexity. CNV studies to date have not been able to consider the genetic variations inside these hundreds of kilobases to megabases of HSDs. Thus, we do not know the exact “genomic scar” of each CNV in individual carriers including additional smaller-scale rearrangements, gene fusions, and copy number changes of paralogs, the diversity HSD rearrangements across different CNV carriers, and the concomitant functional effects. The major aims here are to (1) develop generalizable genome analysis methods to solve this important problem in psychiatric genetics in established cell lines carrying the 16p11.2 deletions and duplications as the first targets of this new approach, (2) to develop high-throughput genotyping assays so that studying the diversity of HSD rearrangements can be applied to expanded groups of affected individuals where only DNA sample (no cell lines) is available and to future cohort association studies, and (3) to investigate the functional effects of HSD rearrangement diversity on CNV biology using cortical organoid models. To facilitate career development and transition to an independent investigator, the following five training goals will be achieved under the support and guidance of the mentorship team: (1) developing expertise in targeted genome assembly analysis and optical DNA mapping; (2) expanding knowledge in developmental neuroscience and pathophysiology of psychiatric disorders; (3) gaining hands-on expertise in neuronal organoid modelling (4) acquiring expertise in chromatin interaction analysis and single-cell RNA expression analysis of neural organoids; (5) gaining experience in grant writing. The hands-on training will primarily take place at Stanford University with training components conducted at Yale and KU Leuven.

项目摘要 拟议的项目是获得关键培训和研究经验的平台 实现成为主要重点的主要学术主要研究员的长期职业目标 开发和应用基因组方法来了解复杂的遗传成分和生物学 神经精神疾病的机制。 大删除或重复的形式（拷贝数变体，CNVS）的形式的染色体畸变， 例如1q21.1、16p11.2和22q11.2的那些是神经精神病学的已知风险因素 疾病。因此，这些大型CNV是研究分子的关键入口点 病因。但是，尚不清楚这些CNV中的每一个都与各种临床结果有关。为了 例如，16p11.2的删除和重复是精神分裂症（SZ）和自闭症的强大风险因素 频谱障碍（ASD）。重复的SZ风险增加了10倍以上，但ASD是 经常进行删除的载体以及重复。大量的人类特异性段 重复（HSD）既构成并介导这些大型“神经精神病学” CNV的形成 由于其高度重复性和复杂性，无法获得当前基因组测序分析。 迄今为止，CNV研究还无法考虑这数百个千倍酶内部的遗传变异 到HSD的巨型群。这是，我们不知道单个载体中每个CNV的确切“基因组疤痕” 包括其他较小规模的重排，基因融合和旁系同源的拷贝数变化， 多样性的HSD重排在不同的CNV载体上，以及伴随的功能效应。 主要目的是（1）开发可概括的基因组分析方法来解决这一重要 携带16p11.2缺失和重复的既定细胞系中精神病遗传学问题 这种新方法的第一个目标，（2）开发高通量基因分型测定，以便研究 HSD重排的多样性可以应用于仅DNA的受影响的个体的扩展组 样本（无细胞系）可用，并将其用于未来的队列关联研究，（3）研究功能 使用皮质器官模型对HSD重排多样性对CNV生物学的影响。 为了促进职业发展并过渡到独立调查员，以下五个培训 在Mentalship团队的支持和指导下将实现目标：（1）发展专业知识 靶向基因组组装分析和光学DNA映射； （2）扩大发展方面的知识 精神疾病的神经科学和病理生理学； （3）获得神经元方面的动手专业知识 器官建模（4）获取染色质相互作用分析和单细胞RNA表达方面的专业知识 分析神经器官； （5）获得赠款写作的经验。动手训练将主要接受 在斯坦福大学（Stanford University）的位置，在耶鲁大学（Yale）和鲁文（Ku Leuven）进行了培训组件。