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: 10429771
• 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/10429771
• 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; base; career; career development; cell type; cohort; digital; established cell line; experience; functional outcomes; genome analysis; genome sequencing; homologous recombination; induced pluripotent stem cell; neuropsychiatric disorder; neuropsychiatry; novel; novel strategies; paralogous gene; psychogenetics; relating to nervous system; 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 建议的项目可作为一个平台，以获取以下方面的主要培训和研究经验： 实现成为一个领先的学术主要研究者的长期职业目标，主要关注 开发和应用基因组方法来了解复杂的遗传成分和生物学特性， 神经精神障碍的机制。 大缺失或重复形式的染色体畸变（拷贝数变异，CNV）， 例如1q21.1、16p11.2和22q11.2上的那些，是神经精神疾病最强的已知危险因素。 紊乱由于这个原因，这些大的CNV作为研究分子生物学的关键切入点。 病因学然而，目前尚不清楚为什么这些CNV中的每一个都与不同的临床结果相关。为 例如，16p11.2的缺失和重复是精神分裂症（SZ）和自闭症的强风险因素 谱系障碍（ASD）。重复导致SZ的风险增加10倍以上，但ASD是 经常出现在缺失和重复的载体中。人类特有的大部分节段性 构成和介导这些大的“神经精神”CNVs形成的复制（HSDs）是 由于其高度的重复性和复杂性，目前的基因组测序分析无法获得。 迄今为止，CNV研究还没有考虑到这数百种酶中的遗传变异 到百万兆的HSDs。因此，我们不知道个体携带者中每个CNV的确切“基因组瘢痕 包括额外的小规模重排、基因融合和旁系同源物的拷贝数变化， 不同CNV携带者之间的HSD重排多样性，以及伴随的功能效应。 本文的主要目的是（1）开发可推广的基因组分析方法来解决这一重要问题。 在已建立的携带16p11.2缺失和重复的细胞系中， 这种新方法的第一个目标，（2）开发高通量基因分型检测，以便研究 HSD重排的多样性可以应用于受影响个体的扩大群体， 样本（无细胞系）可用于未来的队列关联研究，以及（3）研究功能性 使用皮质类器官模型研究HSD重排多样性对CNV生物学的影响。 为了促进职业发展和向独立调查员过渡， 在导师团队的支持和指导下，将实现以下目标：（1）发展以下方面的专业知识 有针对性的基因组组装分析和光学DNA图谱;（2）扩大知识的发展 神经科学和精神疾病的病理生理学;（3）获得神经元疾病的实践专业知识 类器官建模（4）获得染色质相互作用分析和单细胞RNA表达方面的专业知识 神经类器官分析;（5）获得撰写资助的经验。实践培训将主要采取 在斯坦福大学的地方与耶鲁大学和KU鲁汶进行培训部分。