Functional Dissection of CNVs in Neurodevelopmental Traits

神经发育特征中 CNV 的功能剖析

• 批准号: 10107962
• 负责人: Erica Ellen Davis
• 金额: $ 19.13万
• 依托单位: LURIE CHILDREN'S HOSPITAL OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-02-15 至 2021-09-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10107962
• 关键词: Functional; Dissection; CNVs; Neurodevelopmental; Traits

 DESCRIPTION (provided by applicant): Despite major advances in genomic technologies, the integration of genetic data with clinical management remains challenging. This problem is particularly poignant for copy number variants (CNVs), lesions that typically perturb the dosage of dozens of genes and, as recent data have revealed, are major contributors to genetic disorders, most notably neurodevelopmental traits. Recent advances that afford superior resolution in the detection of genomic lesions have accelerated the discovery of CNVs in patients; however, with the exception of rare cases with point mutations of discrete genes within a CNV, the transition from CNV detection to assigning phenotypic contribution of specific genes remains largely intractable. We have taken an orthogonal approach to the problem, grounded on two key observations: a) that some CNVs associated with neurodevelopmental traits exhibit quantitative anatomical phenotypic surrogates; and b) that some CNVs manifest in reciprocal relationships (deletions and duplications of the same or overlapping genomic segment) with either similar or mirroring clinical phenotypes. Grounded on these observations, we have performed systematic overexpression and suppression studies in zebrafish embryos and have identified KCTD13 and CHD1L as the primary drivers of the neuroanatomical phenotypes associated with the 16p11.2 and 1q21.1 CNVs respectively, results that have been substantiated by the subsequent identification of rare atypical de novo deletions in these two genes in patients with autism spectrum disorders (ASD). Here we propose to develop further our tools to systematically dissect other reciprocal CNVs associated with neurocognitive traits. Under a series of filters that select for number of protein encoding genes, and mandate tractable anatomical features that can be recapitulated in zebrafish embryos, we will focus initially on 12 CNVs and assay in vivo the possible contribution of each gene contained within these lesions. Additionally, we will ask whether concomitant dosage misregulation of the primary CNV driver locus and each additional gene within the CNV might influence the expressivity of relevant anatomical, quantitative phenotypes. For the resulting group of candidate or contributing CNV driver genes, we will ask whether these genes a) are also involved in atypical, rare deletions identified by high resolution array comparative genomic hybridization (aCGH) datasets generated from cohorts with an enrichment of neurocognitive phenotypes; and b) bear point mutations in ASD exomes that will be functionally tested using a zebrafish model to assay pathogenicity and direction of effect. Finally, we will ask whether testing of all alleles detected for each transcript in cases and controls might reveal a mutational burden at these loci that is invisible by statistical means alone. Together, these data will identify a number of genes that drive neurocognitive effects in humans and provide an efficient platform for the systematic dissection of CNVs discovered in patient exomes and genomes.

 描述（由申请人提供）：尽管基因组技术取得了重大进展，但遗传数据与临床管理的整合仍然具有挑战性，对于拷贝数变异（CNV）、通常扰乱数十个基因剂量的病变来说，这个问题尤其严重。最近的数据显示，它们是遗传性疾病的主要促成因素，尤其是神经发育特征，在检测基因组病变方面提供了卓越的分辨率，这加速了患者中 CNV 的发现，但极少数情况除外；离散的对于 CNV 中的基因，从 CNV 检测到分配特定基因的表型贡献的转变在很大程度上仍然很棘手，我们基于两个关键观察结果采取了正交方法：a）一些与神经发育特征相关的 CNV 表现出定量的解剖表型。 b) 一些 CNV 表现出具有相似或镜像临床表型的相互关系（相同或重叠基因组片段的删除和重复）。基于这些观察，我们在斑马鱼胚胎中进行了系统的过度表达和抑制研究，并确定 KCTD13 和 CHD1L 分别是与 16p11.2 和 1q21.1 CNV 相关的神经解剖表型的主要驱动因素，这些结果已得到随后鉴定了自闭症谱系障碍（ASD）患者这两个基因中罕见的非典型从头缺失。在此，我们建议进一步开发我们的工具，以系统地进行研究。剖析与神经认知特征相关的其他相互 CNV，在一系列选择蛋白质编码基因的过滤器下，并要求可在斑马鱼胚胎中重现的易于处理的解剖特征，我们将首先关注 12 个 CNV，并在体内分析可能的贡献。此外，我们将询问主要 CNV 驱动基因座和 CNV 内每个附加基因的伴随剂量调节是否可能影响 CNV 的表达性。对于由此产生的候选或贡献 CNV 驱动基因组，我们将询问这些基因 a) 是否也参与由高分辨率阵列比较基因组杂交 (aCGH) 数据集鉴定的非典型、罕见缺失。神经认知表型的富集；b) ASD 外显子组中的点突变将使用斑马鱼模型进行功能测试，以测定致病性和作用方向。检测到 病例和对照中的每个转录本可能会揭示这些基因座的突变负担，而这些基因座仅通过统计手段是看不见的，这些数据将共同识别出许多驱动人类神经认知效应的基因，并为系统性解剖 CNV 提供一个有效的平台。在患者外显子组和基因组中发现。