A Community Zebrafish Resource for Modeling GWAS Biology

用于 GWAS 生物学建模的社区斑马鱼资源

• 批准号: 8609133
• 负责人: Wolfram Goessling
• 金额: $ 85.03万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-01 至 2018-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8609133
• 关键词: Alleles; Animal Model; Bioinformatics; Biological Assay; Biological Models; Biology; Candidate Disease Gene; Chemicals; Communities; Complement; Complex; Computer Simulation; Data; Disease; Evaluation; Foundations; Functional RNA; Gene Transfer Techniques; Genes; Genetic; Genetic Models; Genome; Genotype; Heritability; Human; Human Genetics; Institution; Investigation; Maps; Methods; Metric; Modeling; Organism; Orthologous Gene; Pharmaceutical Preparations; Pharmacology; Phenotype; Physiology; Reagent; Reporter; Research Personnel; Resolution; Resources; Series; Signal Transduction; System; Techniques; Technology; Testing; Tissues; Translations; Variant; Whole Organism; Zebrafish; assay development; chemical genetics; design; disease mechanisms study; disease phenotype; drug discovery; gain of function; gene function; genetic variant; genome wide association study; genome-wide; human disease; in vivo Model; insight; interest; loss of function; mutant; novel; novel marker; public health relevance; response; screening; tool; trait; transcription factor; zinc finger nuclease

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.

描述（由申请人提供）：我们正在提议建立一个用于 GWAS 生物学建模的社区斑马鱼资源，该资源将利用我们机构内斑马鱼遗传学、生物信息学、斑马鱼检测开发、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背后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补充广泛性状的 GWAS 的平台。重要的是，这种方法很容易适应药物反应表型和出现的新特征。具体目标是；目标 1 - 初始可行性评估和测定开发 a) 生物信息学 - 对特征进行初步评估，以评估斑马鱼建模的可行性，并结合真实直向同源物的生物信息学识别、试剂设计以及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 个基因组数据中识别出 [26, 27]）和最新的组织特异性 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) 测定设计-我们将为感兴趣的表型建立代表性和定量测定，并使用调节表型的已知孟德尔基因的已知操作将其锚定到现有的人类基因型和表型。目标 2-跨多个位点的候选基因和非编码变异的系统评估-一旦表型测定得到验证，我们将在斑马鱼中测试每个候选基因和调控序列（可以识别直向同源物）的单独和组合对主要性状的影响[3​​0]。将使用现有突变体、吗啉代和瞬时或稳定转基因对功能丧失和功能获得等位基因进行定量评估。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 位点的因果基因，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）或功能获得等位基因 [31 -33]。此外，在相关的情况下，我们将生成稳定的报告菌株用于后续的遗传或化学筛选。这些内容将免费提供给社区，以加速已完成和正在进行的 GWAS 的翻译。