Leveraging novel methods to improve nonsyndromic cleft lip/palate gene discovery

利用新方法改善非综合征性唇裂/腭裂基因发现

• 批准号: 10676885
• 负责人: JACQUELINE T HECHT
• 金额: $ 16.44万
• 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: 2022-08-04 至 2024-08-03
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10676885
• 关键词: Affect; Alleles; Child; Complex; Congenital Abnormality; Counseling; Data; Data Set; Environmental Risk Factor; Ethnic Origin; Family; Financial Hardship; Foundations; Funding; Future; Genes; Genetic; Genetic Variation; Genome; Heritability; Hispanic; In Vitro; Individual; Medical; Methods; Newborn Infant; Not Hispanic or Latino; Penetrance; Recurrence; Risk; Risk Assessment; Translating; Untranslated RNA; Variant; causal variant; cleft lip and palate; clinical practice; craniofacial; gene discovery; genetic architecture; genome sequencing; genome-wide linkage; high risk; improved; in vivo; insight; nonsyndromic cleft lip with or without cleft palate; notch protein; novel; psychosocial; rare variant; risk variant; segregation; whole genome

PROJECT SUMMARY In this proposal, we will apply robust analytical approaches to whole genome sequencing (WGS) data [obtained from our X01 Gabriella Miller Kids First (GMKF)-funded dataset] from 20 large multigenerational families of Hispanic and nonHispanic white ethnicities to identify variants individually and in aggregate contributing to nonsyndromic cleft lip/palate (NSCLP). NSCLP is a common birth defect annually affecting approximately 135,000 newborns/year worldwide. Despite improvement in treatments, NSCLP imposes significant medical, psychosocial and financial burdens to affected individuals and their families. NSCLP is complex, caused by genetic and environmental factors, and their interactions. It is estimated that ~25% of the genetic liability for NSCLP has been uncovered; however, most of the identified variants reflect common, modest risk-variants often located in noncoding regions of the genome. More recently, it has been suggested that part of the missing heritability for NSCLP lies in rare, high-risk variants, independently or via interactions with common variants. These observations highlight the complexity of NSCLP and difficulty in unraveling risk alleles, and may explain the lack of consistent findings among studies. In this proposal, we will select 20 large and informative families sequenced (WGS) through the X01 mechanism and conduct genome-wide linkage and association, and PRS- informed analyses to assess the contribution of rare and common genetic variation to familial NSCLP. In support of our proposed approach, we have exciting and robust preliminary data showing the identification of a rare variant segregating with NSCLP in a large multiplex family that was modified by common risk variants likely impacting penetrance of the gene. Moreover, we showed that this variant was a null allele and resulted in craniofacial notching mimicking NSCLP. These findings demonstrate the strengths of our approach and the high potential for discovery of novel NSCLP genes/variants. The results of this study will provide novel and important insights about the genetic architecture of NSCLP and lay the foundation for more extensive analysis of WGS data from NSCLP families. The results will also inform putatively causal variants to be used in future functional characterization studies in vitro and in vivo. Ultimately, this study will provide the groundwork for better risk assessment for NSCLP individuals and their families that can be translated into more precise recurrence risk counseling in clinical practice.

项目摘要 在这项提案中，我们将应用强大的分析方法，全基因组测序（WGS）数据[获得 来自我们的X 01 Gabriella米勒儿童第一（GMKF）资助的数据集]，来自20个大型多代家庭， 西班牙裔和非西班牙裔白色种族，以识别个体和总体上有助于 非综合征性唇腭裂（NSCLP）。NSCLP是一种常见的出生缺陷，每年约影响 全球每年有13.5万新生儿。尽管在治疗方面有所改进，但非小细胞肺癌对患者的医疗、 对受影响的个人及其家庭造成心理和经济负担。NSCLP是一种复杂的疾病，由 遗传和环境因素及其相互作用。据估计，约25%的遗传易感性， NSCLP已被发现;然而，大多数已确定的变异反映了常见的，中等风险的变异， 位于基因组的非编码区。最近，有人提出，部分失踪人员 NSCLP的遗传性存在于罕见的高风险变体中，独立地或通过与常见变体的相互作用。 这些观察结果强调了NSCLP的复杂性和解开风险等位基因的困难，并可能解释 研究之间缺乏一致的结果。在这份建议书中，我们将选择20个大的和信息丰富的家庭， 通过X 01机制测序（WGS）并进行全基因组连锁和关联，以及PRS- 知情分析，以评估罕见和常见遗传变异对家族性NSCLP的贡献。支持 在我们提出的方法中，我们有令人兴奋和强大的初步数据显示， 在一个大的多重家族中，与NSCLP一起分离的变异可能被常见的风险变异所修饰， 影响基因的表达。此外，我们发现这种变异是一个无效等位基因， 颅面切迹模仿非小细胞肺癌这些发现证明了我们的方法的优势和高 发现新的NSCLP基因/变体的潜力。这项研究的结果将提供新的和重要的 深入了解NSCLP的遗传结构，为更广泛地分析WGS奠定基础 来自NSCLP家族的数据。这些结果也将告知pupestine因果变异用于未来的功能性 体外和体内表征研究。最终，这项研究将为更好的风险管理提供基础。 评估NSCLP个体及其家庭，可以转化为更精确的复发风险 临床实践中的咨询。