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Streamlined cloning of auditory and vestibular mutants by whole genome sequencing

通过全基因组测序简化听觉和前庭突变体的克隆

基本信息

批准号：
8224539
负责人：
SEAN G MEGASON
金额：
$ 25.43万
依托单位：
HARVARD MEDICAL SCHOOL
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-01-10 至 2013-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8224539
关键词：
Adult Affect Alleles Animal Model Applied Genetics Area Auditory Base Sequence Bioinformatics Biological Chemicals Cloning Computer software DNA Resequencing Defect Development Ear Embryo Embryonic Development Equilibrium Future Gamma Rays Genes Genetic Genetic Polymorphism Genetic Screening Genome Genomics Goals Hair Health Hearing Histocompatibility Testing Human Human Development Individual Insertional Mutagenesis Investments Labyrinth Learning Maps Methods Modeling Molecular Molecular Analysis Morphogenesis Mutagenesis Mutagens Mutate Mutation Natural regeneration Organ Pathway interactions Phenotype Positioning Attribute Publishing Reaction Research Research Personnel Semicircular canal structure Structure Technology Time Vertebrates Zebrafish base cell type cellular transduction cost deafness feeding gene function genetic linkage analysis genome sequencing model organisms databases mutant next generation novel positional cloning prevent research study sound

项目摘要

DESCRIPTION (provided by applicant): Over the last two decades zebrafish has emerged as one of the preeminent model organisms. This rise was in large part due to the promise of using forward genetic screens in a vertebrate animal to discover and elucidate the function of genes relevant to human development and health. Numerous genetic screens have now been performed both for general embryonic morpohological phenotypes as well as more specialized functional screens such as for balance and hearing. These screens have been very successful in identifying mutants and there are now over 6000 described chemically induced mutant lines in zebrafish. However, the gene mutated in these lines has only been identified in less than half the cases due to the current difficulty of positional cloning. The high cost and labor currently required for positional cloning prevents a molecular analysis of many current mutants as well as discouraging future genetic screens. Recent advances in next generation sequencing have reduced the cost of sequencing by several orders of magnitude such that it is now possible to routinely resequence entire genomes. These advances have already revolutionized many areas of genomics yet the way people do positional cloning in zebrafish and other model organisms has changed relatively little. Here we propose to apply next generation sequencing technologies to streamline positional cloning of mutants in model organisms focusing on zebrafish inner ear mutants. Our goal is to reduce the labor and cost of positional cloning by one to two orders of magnitude. We will compare two different approaches for cloning-by-sequencing based on linkage and homozygosity mapping by cloning 10 existing mutants in two mutant classes-semicircular canal morphogenesis and deafness. PUBLIC HEALTH RELEVANCE: Defects in hearing and balance represent a major health problem in humans. Models for these defects can be identified in genetic screens in zebrafish but are currently difficult to molecularly characterize. We will develop an approach to streamline the cloning of such mutants using next generation sequencing.

描述（由申请人提供）：在过去的二十年里，斑马鱼已经成为一种杰出的模式生物。这种增长在很大程度上是由于在脊椎动物中使用正向遗传筛选来发现和阐明与人类发育和健康相关的基因功能的前景。现在已经进行了许多遗传筛选，既用于一般胚胎形态表型，也用于更专门的功能筛选，如平衡和听力。这些筛选在鉴定突变体方面非常成功，现在在斑马鱼中描述了超过6000种化学诱导的突变系。然而，由于目前定位克隆的困难，在这些品系中突变的基因仅在不到一半的情况下被鉴定。目前定位克隆所需的高成本和劳动力阻碍了对许多当前突变体的分子分析，也阻碍了未来的遗传筛选。下一代测序的最新进展已经将测序成本降低了几个数量级，使得现在可以对整个基因组进行常规重测序。这些进步已经彻底改变了基因组学的许多领域，但人们在斑马鱼和其他模式生物中进行定位克隆的方式变化相对较小。在这里，我们建议应用下一代测序技术，以简化模式生物中的突变体定位克隆专注于斑马鱼内耳突变体。我们的目标是将定位克隆的劳动力和成本降低一到两个数量级。我们将比较两种不同的方法克隆测序的基础上连锁和纯合性映射克隆10个现有的突变体在两个突变类半规管形态发生和耳聋。公共卫生相关性：听力和平衡缺陷是人类的主要健康问题。这些缺陷的模型可以在斑马鱼的遗传筛选中鉴定，但目前难以进行分子表征。我们将开发一种方法，以简化克隆这样的突变体使用下一代测序。