Molecular characterization of novel loci for orofacial clefting using canine mode

描述（由申请人提供）： 口面裂是儿童最常见的先天性疾病之一。它们可以作为腭裂（CPO）或唇裂伴或不伴腭裂（CL/P）的孤立病例发生，或与其他出生缺陷相结合。口面裂可以在年轻时通过手术矫正;然而，可能会导致终身的医疗问题和生活质量下降。基因解释了适度的比例口面裂已被确定，但是，大多数情况下，没有分子定义。口面裂也是常见的自然发生的出生缺陷，见于家犬。遗传研究表明，至少在三个不同的狗品种的常染色体隐性遗传模式。这项建议的目的是确定遗传因素，使个人容易口面裂使用狗作为模式生物。 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。短的妊娠窗口期（63天），大量的全同胞和易于DNA样本收集使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允许使用少数受影响的个体有效地绘制致病基因。狗基因组的7 X序列和单核苷酸多态性（SNPs）的相关发现为全基因组关联研究提供了必要的工具。由于个别犬种内的连锁不平衡（LD）程度相对较大，与人类研究相比，需要更少的SNP和更少的DNA样本，以便在单个品种内进行映射时识别显著的遗传关联。我们建议，以确定致病基因和突变的四个位点，导致口面裂的狗。为了实现这一目标，我们将扩大我们目前的DNA样本收集，表型分类和自然发生的裂狗及其亲属的环境数据。将使用基于品种LD的极高密度的新173 K SNP基因分型阵列，使用两个品种内的受影响个体、未受影响对照同胞和无关对照进行全基因组关联分析。精细结构定位和重测序将用于定义导致犬口面裂的四个基因座的候选突变，这将在来自多个品种的表型个体的大型犬DNA样本队列中进行验证。 初步数据表明，这种方法的可行性和实用性的狗作为模型的口面裂。仅使用来自单个品种的16个受影响的样本，通过GWAS确定了两个显著相关的区域，并将其缩小到1 Mb和2.4 Mb的临界区间。通过比较家系成员的基因型，这两个区域被证明是作为独立的简单隐性性状遗传。这两个区域也是新的已知基因参与口面裂形成在人类或啮齿动物。从表型上看，一个区域似乎会导致唇腭裂，而另一个区域只会导致腭裂。这项在狗身上进行的研究有望找到人类口面裂的候选基因和途径。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。通过定义平行的自然发生的疾病的遗传基础，我们希望以前没有涉及这些疾病的基因和途径将被确定。

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.