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: 8530023
• 负责人: DANIKA L BANNASCH
• 金额: $ 50.14万
• 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/8530023
• 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）： 口面部裂是儿童最常见的先天性疾病之一。它们可以作为孤立的腭裂 (CPO) 病例，或伴或不伴腭裂的唇裂 (CL/P) 病例，或与其他出生缺陷合并发生。口面部裂痕可以在年轻时通过手术矫正；然而，可能会出现终生的医疗问题并导致生活质量下降。已经确定了解释一定比例口面部裂痕的基因；然而，大多数病例都没有分子定义。口面部裂也是常见的自然发生的出生缺陷，在家犬中常见。遗传研究表明，至少三种不同的犬种存在常染色体隐性遗传模式。该提案旨在使用狗作为模型生物来确定导致个体易患口面部裂的遗传因素。 家犬提供了独特的哺乳动物模型系统。与其他模式生物不同，狗与我们共享生活环境和医疗保健，并且容易受到自然发生的出生缺陷的影响。较短的妊娠窗口（63 天）、大量的同胞兄弟姐妹以及易于采集的 DNA 样本使该狗成为一个有用的模型系统。从完整的犬基因组序列开发的工具可以利用少数受影响的个体来有效地绘制致病基因图谱。狗基因组的 7X 序列以及相关的单核苷酸多态性 (SNP) 发现为完整的全基因组关联研究提供了必要的工具。由于单个犬种内存在相对较大程度的连锁不平衡 (LD)，与人类研究相比，为了在单个品种内进行绘图时识别显着的遗传关联，需要更少的 SNP 和 DNA 样本。我们建议确定导致狗口颌裂的四个基因座的致病基因和突变。为了实现这一目标，我们将扩大目前的 DNA 样本收集、表型分类和来自自然发生的唇裂狗及其亲属的环境数据。将使用两个品种内受影响的个体、未受影响的对照兄弟姐妹和无关对照进行全基因组关联分析，使用新的 173K SNP 基因分型阵列，该阵列具有基于品种 LD 的极高密度。精细结构图谱和重测序将用于定义导致狗口面部裂的四个位点的候选突变，这些突变将在来自多个品种的表型个体的大量狗 DNA 样本中得到验证。 初步数据证明了这种方法的可行性以及狗作为口颌裂模型的实用性。仅使用来自单一品种的 16 个受影响样本，通过 GWAS 识别出两个显着相关的区域，并将其缩小到每个 1 Mb 和 2.4 Mb 的临界区间。通过比较家庭成员的基因型，这两个区域都被证明是作为独立的简单隐性性状遗传的。就与人类或啮齿动物口面裂形成有关的已知基因而言，这两个区域也是新颖的。从表型上看，一个区域似乎会导致唇裂和腭裂，而另一区域仅导致腭裂。拟议的对狗的研究预计将导致人类口颌裂候选基因和途径的鉴定。狗作为人类出生缺陷模型系统的验证将为这些缺陷的研究开辟新的途径。通过定义平行自然发生的疾病的遗传基础，我们期望能够识别出以前与这些疾病无关的基因和途径。