Integrative Genomic Applications to Understand the Etiology of Unsolved Craniofacial Anomalies

面部或头部的头面部畸形是美国最常见的出生缺陷之一 并代表着巨大的公共卫生负担。尽管投入了相当多的资源来研究 各种颅面部疾病的生物病因学，导致 这些先天异常在很大程度上仍然没有特征性。定义这些背后的遗传病因学 疾病不仅将改善这些疾病的诊断和筛查，而且还将改善治疗。在一个 最近的研究，我们调查了鼻咽癌的遗传病因，这是一种极其罕见的颅面畸形。 完全没有外鼻的。在观察到的这个耳鼻喉科队列中的测序分析 84%的独立耳聋患者中Smchd1罕见杂合性错义突变显著积累 这些病例在60,706名来自外显子组聚集联盟(ExAC)的对照受试者中均未出现。 Smchd1是一种表观遗传调节因子，此前已被认为与肌肉双基因形式有关。 营养不良(FSHD2)，但从未与任何头面部疾病有关。目标1将探索 Smchd1机制导致耳聋，也为功能基因组学提供了宝贵的培训经验 同时使用表观遗传学和转录组分析患者来源的细胞系(Aim 1a)和软骨组织 来自Smchd1击倒斑马鱼(目标1b)。Aim 2将过渡到更常见的头面部疾病 在678例口面部裂(OFC)先证者中寻求新的基因发现 全基因组测序。依靠尖端的WGS分析，我将深入研究突变 谱对于传统的基因测试是神秘的，因此从未在OFC中被表征 一群人。值得注意的是，这些研究将促进自然过渡到独立的R00阶段，这将 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 在基因组结构方面的专业知识，以实现第一个完整的全基因组和全转录组基因 在AIM 3的OFC队列中的发现工作。这将提供对基因组和 Transciptome，这将导致更好的基因发现和机制洞察。总体而言，这个项目 代表着一个独特的培训机会，可以在我职业发展的每个目标领域发展技能 通过获得一套多样化的功能基因组学技术和专业知识，并将为我提供 更广泛地接触到头面部遗传学领域。在完成 格兰特，我将非常适合担任独立教职。此外，虽然这支队伍的训练潜力 项目很高，提出的研究将对颅面遗传学领域产生重大影响，并 在我最终开发自己的独立研究项目时，理想地为未来的拨款提供种子。

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.