Molecular characterization of novel loci for orofacial clefting using canine mode

描述(由申请人提供)： 口腔裂隙是儿童最常见的先天性疾病之一。它们可以作为单独的腭裂病例(CPO)，或伴有或不伴有腭裂的唇裂(CL/P)，或合并其他出生缺陷。口腔裂隙可以在年轻的时候通过手术矫正；然而，可能会有终生的医疗问题，并因此降低生活质量。解释一小部分口腔裂隙的基因已经被确定；然而，大多数病例没有分子定义。口腔裂也是常见的自然发生的出生缺陷，在家犬，家犬。遗传研究表明，至少在三个不同的犬种中存在常染色体隐性遗传模式。这项提议旨在利用狗作为模式生物来识别易患口裂的遗传因素。家犬提供了一种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。较短的妊娠窗口期(63天)，大量完整的兄弟姐妹，以及DNA样本的轻松采集，使这只狗成为一个有用的模型系统。从完整的犬类基因组序列开发的工具可以使用很少受影响的个体有效地绘制致病基因的图谱。狗基因组的7X序列和相关的单核苷酸多态(SNPs)的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SNPs和更少的DNA样本，以便在单个犬种内定位时识别显著的遗传关联。我们建议确定引起狗的口裂的四个基因座的致病基因和突变。为了实现这一目标，我们将扩大我们目前收集的DNA样本、表型分类和自然发生的裂狗及其亲属的环境数据。将使用新的173K SNP基因分型阵列对两个品种内的患病个体、未受影响的对照同胞和无关对照进行全基因组关联分析，该阵列基于品种LD的极高密度。精细结构图谱和重新测序将用于确定导致狗的口面部裂伤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量狗DNA样本中得到验证。初步数据证明了该方法的可行性和犬作为口腔颌面裂模型的实用性。仅使用来自单个品种的16个受影响的样本，GWAS确定了两个显著相关的区域，并将其缩小到分别为1Mb和2.4Mb的临界间隔。通过比较家系成员的基因类型，表明这两个区域是作为独立的简单隐性性状遗传的。这两个区域在涉及人类或啮齿动物口腔裂隙形成的已知基因方面也是新的。从表观上看，一个区域似乎会导致唇腭裂，而另一个区域则只会导致腭裂。这项拟议中的狗身上的工作有望导致识别出人类口面部裂开的候选基因和途径。狗被确认为人类出生缺陷的模型系统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疾病的遗传基础，我们预计将识别以前与这些疾病无关的基因和途径。

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.