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.

摘要 口面裂（OFC，包括唇裂-CL，腭裂-CP，或两者-CLP）是最常见的 人类颅面畸形，影响全世界约1/700的新生儿，因此是世界上最严重的颅面畸形之一。 最常见的结构性出生缺陷。OFC对公共卫生有重大影响， 相关的发病率和死亡率。患有眶额皮层的普通儿童最初面临喂养困难， 6次手术，住院30天，接受5年的正畸治疗，并参加正在进行的 语言治疗，导致估计总的终身治疗费用约为20万美元。此外，个人 出生时患有眶额肌痛的人，心理健康问题的发生率增加， 生活和其他疾病的风险较高（特别是包括乳腺癌，脑癌和结肠癌），以及婴儿 死亡率（特别是在发展中国家，获得医疗保健的机会可能有限）。OFC是 病因复杂，由遗传变异、环境暴露及其相互作用引起。基因组 结合测序结果的广泛关联研究已经鉴定了至少35个基因/区域， 多个独立研究的全基因组意义，但这些结果只占一小部分 遗传性随着全基因组测序（WGS）的可用性，罕见变异研究正在出现 数据集，但罕见变异的功能验证是必不可少的，以产生必要的支持，以链接这些 基因/变异OFC，了解OFC背后的生物学，将关联信号转化为准确的 风险预测，并最终开发和/或改进治疗。这一新的总体目标 合作项目是确定在我们的大型研究中发现的罕见风险变体的功能意义。 OFC家族和对照的资源。这个新项目的拟议目标将有助于实现我们的整体目标。 目标.我们将利用我们的OFC WGS资源（2，078例OFC病例/父母三人组）来发现新的基因组风险 变异与创新的分析，强调单核苷酸变异（SNV），结构变异（SV）， 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了一种新的 一种在小鼠中快速验证推定致病性变体的方法，从而使得能够使用哺乳动物 该系统用于变体验证和更详细地研究所产生的裂缝表型。