Integrative Genomic Applications to Understand the Etiology of Unsolved Craniofacial Anomalies

在美国，面部或头部的颅面畸形是最常见的出生缺陷之一 并且代表了巨大的公共卫生负担。尽管投入了相当多的资源进行研究， 各种颅面疾病的生物学病因，导致颅面疾病的机制 这些先天性异常在很大程度上仍没有特征。确定这些背后的遗传病因 疾病将不仅改善这些疾病的诊断和筛查，而且改善治疗。中 最近的一项研究，我们调查了遗传病因背后的鼻，一个非常罕见的颅面畸形 其定义为完全没有外鼻。在此arhinia队列中观察到的测序分析 在84%的独立的鼻息肉病患者中，SMCHD1中罕见杂合错义突变的显著积累 这些病例在来自外显子组聚集联盟（ExAC）的60，706名对照受试者中均不存在。 SMCHD1是一种表观遗传调节因子，以前曾被认为与肌肉萎缩症的双基因形式有关。 营养不良（FSHD 2），但从未与任何颅面疾病。目标1将探讨 机制SMCHD1导致鼻，也提供了宝贵的培训经验，在功能基因组学 使用患者来源的细胞系（Aim 1a）和软骨组织的表观遗传学和转录组分析 来自smchd 1敲除斑马鱼（Aim 1b）。目标2将过渡到更常见的颅面疾病， 在678例患有口面裂（OFC）的先证者中寻找新的基因发现， 全基因组测序（WGS）。依靠最先进的WGS分析，我将深入研究 对传统基因检测来说是神秘的，因此从未在OFC中表征过 队列。值得注意的是，这些研究将促进自然过渡到独立的R00阶段， 将K99期间在功能基因组学和颅面生物学方面获得的专业知识与我现有的 在基因组结构的专业知识，执行第一个整合的全基因组和全转录组基因 Aim 3中OFC队列的发现工作。这将为基因组和 transciptome，这将导致上级基因发现和机制的洞察力。总的来说，这个项目 代表了一个独特的培训机会，以发展我的职业发展的每个目标领域的技能 通过获得各种功能基因组学技术的访问和专业知识，并将为我提供 更广泛地接触颅面遗传学领域。完成K99培训后， 如果我同意的话，我会很适合一个独立的教师职位。此外，虽然培训的潜力， 项目是高的，提出的研究将对颅面遗传学领域产生重大影响， 理想的种子未来的赠款，因为我最终开发自己的独立研究计划。

Craniofacial abnormalities of the face or head are among the most common birth defects in the United States and represent a large public health burden. Despite a considerable commitment of resources to research on the biological etiology underlying a diverse spectrum of craniofacial disorders, the mechanisms leading to these congenital abnormalities remains largely uncharacterized. Defining the genetic etiology behind these disorders will not only improve diagnosis and screenings of these disorders, but also improve treatment. In a recent study, we investigated the genetic etiology behind arhinia, an extremely rare craniofacial malformation defined by the complete absence of the external nose. Sequencing analysis within this arhinia cohort observed a significant accumulation of rare heterozygous missense mutations in SMCHD1 in 84% of independent arhinia cases none of which were present in 60,706 control subjects from the exome aggregation consortium (ExAC). SMCHD1 is an epigenetic regulator that has been previously been implicated in a digenic form of muscular dystrophy (FSHD2), but has never been associated with any craniofacial disorders. Aim 1 will explore the mechanism SMCHD1 causes arhinia and also provide an invaluable training experience in functional genomics using both epigenetic and transcriptome analyses of patient derived cell lines (Aim 1a) and cartilage tissue from smchd1 knockdown zebrafish (Aim 1b). Aim 2 will transition into more common craniofacial disorders by pursuing novel gene discovery in 678 trios with an orofacial cleft (OFC) affected proband that have undergone whole genome sequencing (WGS). Relying on cutting edge WGS analysis, I will delve into the mutational spectrum that is cryptic to conventional genetic testing and therefore has never been characterized in an OFC cohort. Notably, these studies will facilitate a natural transition into the independent R00 phase, which will bridge the expertise acquired in functional genomics and craniofacial biology during the K99 with my existing expertise in genome structure to perform the first integrated whole-genome and whole-transcriptome gene discovery effort in an OFC cohort in Aim 3. This will provide an unprecedented view of both the genome and transciptome, which will lead to superior gene discovery and mechanistic insight. Overall, this project represents a unique training opportunity to develop skills in each of my targeted areas of career development by gaining access and expertise in a diverse set of functional genomics technology and will provide me with broader exposure to the field of craniofacial genetics. Upon completion of the K99 training proposed in the grant, I will be well suited for an independent faculty position. Moreover, while the training potential of the project is high, the studies proposed will have a significant impact on the field of craniofacial genetics and are ideal to seed future grants as I ultimately develop my own independent research program.