A Community Zebrafish Resource for Modeling GWAS Biology

描述（由申请人提供）：我们正在申请一个社区斑马鱼资源，用于建模GWAS生物学，该资源将利用我们机构在斑马鱼遗传学，生物信息学，斑马鱼分析开发，遗传建模和机制研究方面的现有专业知识。这些研究将为探索人类常见疾病表型的基因网络奠定基础，并在斑马鱼中建立高通量生物学，作为在广泛性状上补充GWAS的平台。重要的是，这种方法很容易适应药物反应表型和新特征的出现。具体目标是；a)生物信息学——对特征进行初步评估，以评估在斑马鱼中建模的可行性，并结合生物信息学对真正同源物的鉴定、试剂设计和可能的候选物的计算机优先级排序。此外，我们将专门探索候选因果snp（从1000个基因组数据中确定[26,27]）与最新的组织特异性ENCODE图谱之间的关系，以定义可能受常见变异影响的转录因子网络[28,29]。b)试验设计-我们将为感兴趣的表型建立具有代表性的定量分析，并使用已知调节表型的已知孟德尔基因的已知操作将这些分析固定到现有的人类基因型和表型上。目标2-跨多个位点的候选基因和非编码变异的系统评估-一旦表型分析得到验证，我们将在斑马鱼中测试每个候选基因和调控序列（其中同源物可以被识别），以确定它们单独和组合对主要性状[30]的影响。将利用现有突变体、morpholinos和瞬时或稳定转基因，对功能等位基因的丧失和获得进行定量评估。我们建议每年研究大约15-20个GWAS位点。目标3：为下游发现建立斑马鱼模型——一旦我们建立了每个GWAS基因座的致病基因，我们将为每个基因开发稳定的功能丧失（使用TALEN或锌指核酸酶技术）或功能等位基因的获得[31 -33]。此外，在相关的情况下，我们将产生稳定的报告菌株，用于后续的遗传或化学筛选。这些代码将免费提供给社区，以加速完成和正在进行的GWAS的翻译。

DESCRIPTION (provided by applicant): We are proposing a Community Zebrafish Resource for Modeling GWAS Biology that will exploit existing expertise within our institutions in zebrafish genetics, bioinformatics, zebrafish assay development, genetic modeling and mechanistic studies. These studies will lay the foundation for exploration of the gene networks underlying common human disease phenotypes, and establish high-throughput biology in the zebrafish as a platform to complement GWAS across a broad range of traits. Importantly, this approach is readily adapted to drug response phenotypes and novel traits as they emerge. The Specific Aims are; Aim 1-Initial feasibility assessment and assay development a) Bioinformatics-An initial evaluation of the traits to assess the feasibility of modeling in the zebrafish combined with bioinformatic identification of true orthologs, reagent design and where possible in silico prioritization of candidates. In addition we will specifically explore the relationships between candidate causal SNPs (identified from 1000 genomes data [26, 27]) and the latest tissue-specific ENCODE maps to define the transcription factor networks that may be impacted by the common variants [28, 29]. b) Assay design-We will build representative and quantitative assays for the phenotypes of interest, and anchor these to existing human genotypes and phenotypes using known manipulations of known Mendelian genes regulating the phenotype. Aim 2-Systematic evaluation of candidate genes and non-coding variants across multiple loci-Once the phenotypic assays have been validated, we will test in the zebrafish each of the candidate genes and regulatory sequences (where the orthologs can be identified) for their effects alone and in combination on the primary trait [30]. Quantitative assessments will be generated for loss of function and gain of function alleles, using existing mutants, morpholinos and transient or stable transgenesis. We propose to study approximately 15-20 GWAS loci per year. Aim 3-Establishing zebrafish models for downstream discovery-Once we have established the causal genes underlying each GWAS locus, we will develop stable loss of function (using TALEN or zinc finger nuclease technology) or gain of function alleles for each gene [31 -33]. In addition, where relevant we will generate stable reporter strains for subsequent genetic or chemical screens. These lines will be made freely available to the community to accelerate the translation of completed and ongoing GWAS.