Genomic Risk Variants in Orofacial Clefting: Discovery and Functional Validation

口颌面裂的基因组风险变异：发现和功能验证

• 批准号: 10560719
• 负责人: Mary L. Marazita
• 金额: $ 75.01万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-12-21 至 2027-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10560719
• 关键词: Affect; Biological Models; Biology; CRISPR/Cas technology; Caring; Child; Cleft Lip; Cleft Palate; Code; Colon Carcinoma; Complex; Congenital Abnormality; Coupled; Craniofacial Abnormalities; Data; Data Set; Developing Countries; Development; Dideoxy Chain Termination DNA Sequencing; Disease; Embryo; Environmental Exposure; Etiology; Face; Family; Gene Expression; Genes; Genomics; Genotype; Goals; Harvest; Heritability; Histology; Hospitals; Human; Incidence; Individual; Infant Mortality; Investigation; Life; Link; Malignant neoplasm of brain; Medical; Mental Health; Morbidity - disease rate; Morphology; Mus; Mutation; Newborn Infant; Nucleotides; Operative Surgical Procedures; Orthodontic; Parents; Pathway interactions; Phenotype; Public Health; Publishing; Research; Resources; Risk; Signal Transduction; Single Nucleotide Polymorphism; Speech Therapy; Structural Congenital Anomalies; Structure; System; Testing; The Jackson Laboratory; Translating; Treatment Cost; Validation; Variant; X-Ray Computed Tomography; causal variant; comorbidity; cost effective; craniofacial; de novo mutation; digital; feeding; flexibility; follow-up; gene discovery; genetic architecture; genetic variant; genome sequencing; genome wide association study; genome-wide; high risk; improved; innovation; insertion/deletion mutation; malignant breast neoplasm; member; microCT; mortality; mouse model; novel; novel strategies; orofacial cleft; rare variant; risk prediction; risk variant; targeted sequencing; whole genome

ABSTRACT Orofacial clefts (OFCs, comprising cleft lip-CL, cleft palate-CP, or both-CLP) are the most common craniofacial anomalies in humans, affecting approximately 1 in 700 newborns worldwide, and are thus one of the most common structural birth defects. There are substantial public health impacts of OFCs, due to associated morbidity and mortality. An average child with an OFC initially faces feeding difficulties, undergoes 6 surgeries, spends 30 days in hospital, receives 5 years of orthodontic treatment, and participates in ongoing speech therapy, leading to an estimated total lifetime treatment cost of about $200,000. Further, individuals born with an OFC have an increased incidence of mental health problems, higher mortality rates at all stages of life and higher risk for other disorders (notably including breast, brain, and colon cancers), and higher infant mortality (particularly in developing countries where access to medical care may be limited). OFCs are etiologically complex, resulting from genetic variants, environmental exposures, and their interactions. Genome wide association studies coupled with sequencing results have identified at least 35 genes/regions achieving genome-wide significance from multiple independent studies but these results only account for a fraction of heritability. Rare variant studies are emerging with the availability of whole genome sequencing (WGS) datasets, but functional validation of rare variants is essential to generate the support necessary to link these genes/variants to OFCs, to understand the biology behind OFCs, to translate association signals into accurate risk predictions, and ultimately to develop and/or improve therapies. The overall goal of this new collaborative project is to identify the functional significance of rare risk variants identified in our large resource of OFC families and controls. The proposed aims of this new project will help achieve our overall goal. We will utilize our OFC WGS resources (2,078 OFC case/parent trios) to discover new genomic risk variants with innovative analyses emphasizing single nucleotide variants (SNVs), structural variants (SVs), and indels. For functional validation, this new project will take advantage of the high-efficiency and flexibility of CRISPR/Cas9 technology: research team members at the Jackson Laboratory have developed a novel approach to rapidly validate putative causative variants in the mouse, thus enabling the use of a mammalian system for both variant validation and for more detailed investigation of the resulting cleft phenotypes.

抽象的 口面裂（OFC，包括唇裂 - CL、腭裂 - CP 或两者 - CLP）是最常见的 人类颅面异常，影响全世界大约七百分之一的新生儿，因此是其中之一 最常见的结构性出生缺陷。 OFC 对公共健康产生重大影响，原因如下： 相关的发病率和死亡率。患有 OFC 的普通儿童最初会面临喂养困难，经历 6次手术，住院30天，接受5年正畸治疗，并参加正在进行的 言语治疗，预计终生治疗总费用约为 200,000 美元。此外，个人 出生时患有 OFC 的人心理健康问题的发生率更高，各个阶段的死亡率也更高 生命和其他疾病（特别是乳腺癌、脑癌和结肠癌）的风险较高，以及婴儿的死亡率更高 死亡率（特别是在获得医疗服务的机会可能有限的发展中国家）。 OFC 是 病因复杂，由遗传变异、环境暴露及其相互作用造成。基因组 广泛关联研究结合测序结果已确定至少 35 个基因/区域实现 多个独立研究的全基因组意义，但这些结果只占一小部分 遗传力。随着全基因组测序 (WGS) 的出现，稀有变异研究不断涌现 数据集，但罕见变体的功能验证对于生成链接这些数据所需的支持至关重要 OFC 的基因/变体，了解 OFC 背后的生物学，将关联信号转化为准确的信号 风险预测，并最终开发和/或改进疗法。此次新政的总体目标是 合作项目的目的是确定我们大型研究中发现的罕见风险变异的功能意义 OFC 系列和控制资源。这个新项目的拟议目标将有助于实现我们的总体目标 目标。我们将利用我们的 OFC WGS 资源（2,078 个 OFC 病例/父母三人组）来发现新​​的基因组风险 具有创新分析的变异，强调单核苷酸变异（SNV）、结构变异（SV）和 插入缺失。对于功能验证，这个新项目将利用 CRISPR/Cas9技术：杰克逊实验室的研究团队成员开发出一种新颖的 快速验证小鼠中假定的致病变异的方法，从而能够使用哺乳动物 用于变异验证和对所产生的裂口表型进行更详细研究的系统。