Oral Clefts: Moving from Genome Wide Studies Toward Functional Genomics

口腔裂隙：从全基因组研究转向功能基因组学

• 批准号: 8268931
• 负责人: Terri H Beaty
• 金额: $ 19.79万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-21 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8268931
• 关键词: Alcian Blue; Animal Model; Animals; Binding Sites; Biological Process; Branchial arch structure; Candidate Disease Gene; Cartilage; Cephalic; Chromatin; Cleft Lip; Cleft Palate; Complex; Congenital Abnormality; Data; Data Set; Deposition; Embryo; Environmental Exposure; Environmental Risk Factor; Etiology; Exons; Fertilization; Gene Expression; Gene Frequency; Genes; Genetic; Genome; Genomic Imprinting; Genotype; Head; Human; In Situ Hybridization; Influentials; International; Introns; Life; Linkage Disequilibrium; Measurable; Mesenchyme; Methylation; MicroRNAs; Modeling; Molecular Profiling; Mutation; Neural Crest Cell; Nucleotides; Parents; Pathway interactions; Phenotype; Polymorphic Microsatellite Marker; Principal Investigator; Regulation; Research; Research Proposals; Resources; Risk; Role; Sequence Analysis; Signal Pathway; Signal Transduction; Singapore; Staining method; Stains; Techniques; Technology; Testing; Tissues; Universities; Untranslated Regions; Variant; Work; Zebrafish; bisulfite; bone; chromatin immunoprecipitation; cleft lip and palate; data management; design; follow-up; functional genomics; gene function; gene interaction; genome wide association study; genome-wide; imprint; in vivo; interest; loss of function; mRNA capping; malformation; novel marker; oral cleft; public health relevance; response; transcription factor; transmission process

DESCRIPTION (provided by applicant): We will follow up on signals from a genome wide association study (GWAS) of oral clefts now being conducted with support from UOl-DE-004425; "International Consortium to Identify Genes & Interactions Controlling Oral Clefts", 2007-2009; TH Beaty. Oral clefts are among the most common human birth defects and have a complex and heterogeneous etiology. Genotyping for this project should be completed in early 2009 and our analysis will identify genes influencing risk directly those acting only in the presence of an environmental risk factor, and/or genes showing measurable parent-of-origin effects which may represent imprinting. In this response to the FaceBase initiative (RFA-DE-09-003) we will build upon our GWAS results by using high throughput sequencing (HTS) techniques of genes/regions yielding statistical evidence of linkage and disequilibrium (Aim 1) and to conduct functional genomic studies of these same genes to understand how they act in vivo using the zebrafish model (Aim 2). We will first focus on genes identified through analysis of single nucleofide polymorphic (SNP) markers from our GWAS and will use HTS to identify all variants (rare mutations and novel markers) that may cause oral clefts. We will then undertake a systematic analysis of 60.000 markers in regions of known copy number variants (CNV) available on this platform, to test and sequence genes that may influence risk through structural variation. In our Aim 2, we will use the zebrafish for expression profiling and loss-of-function analyses of genes identified from our GWAS and sequenced in Aim 1. We will perform further functional studies including expression array, miRNA and/or ChlP-seq analysis. This functional genomics work will identify genes expressed in zebrafish head mesenchyme, cranial neural crest cells, pharyngeal arches, neurocranium and/or other relevant tissues using in situ hybridization and cartilage/bone staining methods in normal embryos and knockdown morphants. We will also gather further functional information via global gene and miRNA expression profiles to identify possible networks or pathways involving interacting genes, and explore methylation/imprinting miRNA regulation and/or chromatin targeting of selected genes. PUBLIC HEALTH RELEVANCE: This project is designed to follow up evidence from a genome wide study of oral clefts (cleft lip, cleft palate & cleft lip and palate) in a large international study of humans by sequencing specific genes to identify causal variants/mutations and using an animal model to better define how these genes function in a living animal.

描述（由申请人提供）：我们将跟进目前在UOL-DE-004425的支持下进行的基因组广泛协会研究（GWAS）的信号； “识别控制口腔裂缝的基因和互动的国际财团”，2007-2009； th狂。口腔裂缝是人类最常见的先天缺陷之一，具有复杂且异质的病因。该项目的基因分型应在2009年初完成，我们的分析将确定直接影响风险的基因，直接在存在环境危险因素的情况下和/或显示出可能代表印记的可能性父母效应的基因。在对面部库计划（RFA-DE-09-003）的这种反应中，我们将通过使用高吞吐量测序（HTS）技术（HTS）技术来依靠我们的GWAS结果，从而产生了链接和不平衡的统计证据（AIM 1）（AIM 1）（AIM 1）（AIM 1）并使用这些相同基因的功能性基因研究，以实现Zebraff的功能基因研究（Zebraf）。我们将首先专注于通过分析GWAS的单核苷多态性（SNP）标记来识别的基因，并将使用HTS来识别可能导致口腔裂口的所有变体（稀有突变和新颖的标记）。然后，我们将对该平台上可用的已知拷贝数变体（CNV）区域的60.000标记进行系统分析，以测试可能通过结构变化影响风险的序列基因。在我们的目标2中，我们将使用斑马鱼对从我们的GWAS鉴定的基因进行表达分析和功能丧失分析，并在AIM 1中进行了测序。我们将进行进一步的功能研究，包括表达阵列，miRNA和/或CHLP-seq分析。这项功能性基因组学工作将鉴定在斑马鱼头间充质，颅神经rest细胞，咽弓，神经弓和/或其他相关组织中使用原位杂交以及正常胚胎中的软骨/骨染色方法。我们还将通过全局基因和miRNA表达谱收集进一步的功能信息，以识别涉及相互作用基因的可能网络或途径，并探索甲基化/烙印miRNA调节和/或染色质靶向所选基因。 公共卫生相关性：该项目旨在跟进一项对口腔裂口（唇裂，唇裂和唇裂唇裂和pa）的基因组广泛研究的证据，这是通过对人类进行的大型国际研究，通过对特定基因进行测序以识别因果变体/突变，并使用动物模型来更好地定义这些基因在生物动物中的作用。