Molecular characterization of novel loci for orofacial clefting using canine mode

使用犬模式对口面部裂新位点进行分子表征

• 批准号: 8337311
• 负责人: DANIKA L BANNASCH
• 金额: $ 52.23万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-22 至 2015-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8337311
• 关键词: Affect; Age; Animal Housing; Animal Model; Biological Models; Breeding; Canis familiaris; Caring; Child; Classification; Cleaved cell; Cleft Lip; Cleft Palate; Cleft lip with or without cleft palate; Complex; Congenital Abnormality; Congenital Disorders; DNA; DNA Databases; DNA Resequencing; Data; Defect; Development; Disease; Environment; Etiology; Evaluation; Family member; Gene Mutation; Genes; Genetic; Genome; Genomics; Genotype; Goals; Human; Individual; Inheritance Patterns; Inherited; Lead; Life; Linkage Disequilibrium; Mammalian Genetics; Maps; Measures; Medical; Modeling; Molecular; Mutation; Pathway interactions; Phenotype; Physiological; Population; Positioning Attribute; Predisposing Factor; Predisposition; Pregnancy; Preventive; Quality of life; Relative (related person); Research; Resolution; Rodent; Sampling; Siblings; Single Nucleotide Polymorphism; Structure; System; Validation; Work; base; cleft lip and palate; cohort; density; dog genome; genetic association; genome sequencing; genome wide association study; novel; offspring; orofacial; recessive genetic trait; sample collection; tool

DESCRIPTION (provided by applicant): Orofacial clefts are one of the most common congenital disorders seen in children. They can occur as isolated cases of cleft palate (CPO), or cleft lip with or without cleft palate (CL/P), or in combination with other birth defects. Orofacial clefts can be surgically corrected at a young age; however, there can be lifelong medical issues and decreased quality of life as a result. The genes explaining a modest percentage of orofacial clefts have been identified; however, the majority of the cases are not molecularly defined. Orofacial clefts are also common naturally occurring birth defects seen in the domestic dog, Canis familiaris. Inheritance studies have demonstrated an autosomal recessive inheritance pattern in at least three different dog breeds. This proposal aims to identify genetic factors that predispose individuals to orofacial clefts using the dog as a model organism. The domestic dog provides a unique mammalian model system. Unlike other model organisms, dogs share our living environment and medical care and are susceptible to naturally occurring birth defects. A short gestational window (63 days), large litters of full siblings and ease of DNA sample collection make the dog a useful model system. Tools developed from the complete canine genome sequence allow efficient mapping of disease-causing genes using few affected individuals. The 7X sequence of the dog genome and the associated discovery of single nucleotide polymorphisms (SNPs) have provided the necessary tools for complete genome wide association studies. Due to the relatively large extent of linkage disequilibrium (LD) within individual dog breeds, many fewer SNPs and fewer DNA samples are needed compared to human studies in order to identify significant genetic associations when mapping within a single breed. We propose to identify the causative genes and mutations for four loci that cause orofacial clefting in the dog. In order to accomplish this, we will expand our current sample collection of DNA, phenotypic classification and environmental data from naturally occurring cleft dogs and their relatives. Genome wide association analysis will be performed using affected individuals, unaffected control siblings and unrelated controls within two breeds using a new 173K SNP genotyping array which is extremely high density based on breed LD. Fine structure mapping and resequencing will be used to define candidate mutations for four loci causing orofacial clefting in dogs which will be validated in large cohorts of dog DNA samples from phenotyped individuals from multiple breeds. Preliminary data demonstrates the feasibility of this approach and the utility of the dog as a model for orofacial clefts. Using only 16 affected samples from a single breed, two significantly associated regions were identified by GWAS and narrowed to critical intervals of 1 Mb and 2.4 Mb each. By comparing genotypes of family members, both regions were shown to be inherited as independent simple recessive traits. Both regions are also novel with respect to known genes involved with orofacial cleft formation in humans or rodents. Phenotypically, one region appears to cause cleft lip and palate while the other causes cleft palate only. The proposed work in the dog is expected to lead to the identification of genes and pathways that are candidates for orofacial clefting in humans. The validation of the dog as a model system for human birth defects will open new avenues for the studies of these defects. By defining the genetic basis for parallel naturally-occurring disorders, we expect that genes and pathways not previously implicated in these diseases will be identified.

描述（由申请人提供）： 口面裂缝是儿童中最常见的先天性疾病之一。它们可以作为孤立的裂口（CPO）的孤立病例，或带有或不带有left裂（Cl/p）的left裂，或与其他先天缺陷结合使用。可以在年轻的时候通过手术纠正口腔裂。但是，结果可能存在终生的医疗问题和生活质量下降。已经鉴定出了解释的小比例裂口的基因；但是，大多数病例尚未分子定义。口面裂缝也是常见的自然发生的天然出生缺陷。继承研究表明，至少三种不同的狗品种中，常染色体隐性遗传模式。该提案旨在确定使用狗作为模型生物体的遗传因素，使个人容易使人偏爱。 家犬提供了独特的哺乳动物模型系统。与其他模型生物不同，狗可以共享我们的生活环境和医疗保健，并且容易出现自然存在的先天缺陷。一个短的妊娠窗口（63天），大量的完整兄弟姐妹和易于DNA样品收集的垃圾使狗成为有用的模型系统。从完整的犬基因组序列开发的工具可以使用很少的受影响的个体对引起疾病的基因进行有效映射。狗基因组的7次序列以及单核苷酸多态性（SNP）的相关发现为完整的基因组广泛关联研究提供了必要的工具。由于单个狗品种中的连锁不平衡（LD）的程度相对较大，因此与人类研究相比，需要较少的SNP和更少的DNA样品，以便在单个品种中映射时鉴定出重要的遗传关联。我们建议确定四个基因座的因果基因和突变，从而引起狗的口面裂。为了实现这一目标，我们将扩大当前的DNA样本集合，表型分类和来自自然存在的裂犬及其亲戚的环境数据。将使用受影响的个体，未受影响的对照兄弟姐妹和两个品种内的无关对照进行基因组宽的关联分析，使用新的173K SNP基因分型阵列，该阵列基于品种LD，其密度极高。精细的结构映射和重新取证将用于定义四个基因座的候选突变，从而导致狗的口面裂纹，这些突变将在大量的狗DNA样本中得到来自多个品种的表型个体的大量狗DNA样品的验证。 初步数据证明了这种方法的可行性以及狗作为口面裂隙的模型的实用性。仅使用来自单个品种的16个受影响的样品，通过GWAS鉴定了两个显着相关的区域，并缩小到1 MB和2.4 MB的临界间隔。通过比较家庭成员的基因型，两个区域被证明是独立的简单隐性特征。对于人类或啮齿动物中与口面裂的形成相关的已知基因，这两个区域也都是新颖的。在表型上，一个区域似乎引起嘴唇和口感，而另一个区域仅引起left裂。预计狗的拟议作品将导致对人类口面裂的候选基因和途径的识别。将狗作为人类出生缺陷的模型系统的验证将为这些缺陷的研究打开新的途径。通过定义平行自然疾病的遗传基础，我们希望将发现以前不涉及这些疾病的基因和途径。