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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要拟议的项目作为获得关键培训和研究经验的平台实现成为主要关注的领先学术首席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。大量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，是已知的最强的神经精神危险因素因此，这些大型 CNV 成为研究分子疾病的关键切入点。然而，目前尚不清楚为什么这些 CNV 与不同的临床结果相关。例如，16p11.2 的缺失和重复是精神分裂症 (SZ) 和自闭症的强烈危险因素谱系障碍 (ASD) 会使患精神分裂症的风险增加 10 倍以上，但 ASD 是频繁出现于缺失和重复的大片人类特异性片段的携带者中。构成并介导这些大型“神经精神”CNV 形成的重复（HSD）是由于高度重复性和复杂性，当前的基因组测序分析无法进行。迄今为止，CNV 研究还无法考虑这数百个碱基内的遗传变异因此，我们不知道个体携带者中每个 CNV 的确切“基因组疤痕”。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 载体之间的多样性 HSD 重排，以及伴随的功能效应。这里的主要目标是（1）开发通用的基因组分析方法来解决这个重要问题已建立的携带 16p11.2 缺失和重复的细胞系中存在精神遗传学问题这种新方法的首要目标是（2）开发高通量基因分型测定法，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，其中只有 DNA 样本（无细胞系）可用并用于未来的队列关联研究，以及（3）研究功能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的过渡，以下五项培训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： (2) 拓展知识的发展精神疾病的神经科学和病理生理学；（3）获得神经元方面的实践专业知识；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的分析；（5）获得资助写作的经验。在斯坦福大学获得学位，并在耶鲁大学和鲁汶大学进行培训。