New technologies for accurate capture and sequencing of repeat-associated regions

用于精确捕获和测序重复相关区域的新技术

• 批准号: 10308722
• 负责人: Alan P Boyle
• 金额: $ 22.58万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-01 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10308722
• 关键词: 3-Dimensional; Automobile Driving; Biological Assay; Brain; Cell physiology; Chromatin; Code; DNA Insertion Elements; DNA Transposable Elements; Data; Development; Disease; Effectiveness; Elements; Evolution; Failure; Foundations; Frequencies; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Variation; Genome; Goals; Human; Human Biology; Human Genome; L1 Elements; Length; Location; Maps; Measurement; Measures; Mediating; Molecular Computations; Mosaicism; Mutagenesis; Nature; Outcome; Phenotype; Play; Population; Regulation; Repetitive Sequence; Research; Retinal blind spot; Role; Shapes; Somatic Cell; Structure; Techniques; Technology; Untranslated RNA; Work; base; cost effective; disease phenotype; follow-up; genome sequencing; human disease; improved; interest; nanopore; nervous system disorder; new technology; whole genome

Project Summary While often ignored in analysis, repetitive regions of the genome and their association with disease is becoming more apparent in recent years. Part of the resurgence of interest in these regions is the availability of new tech- nologies to sequence them and accurately map their location. Indeed, classes of transposable elements have been shown to be polymorphic in the population indicating both their continued activity in shaping our genomes and their propensity to be genetic drivers of phenotype. This has been especially true in neurologic disorders, where transposable elements are not only polymorphic but actively moving in somatic cells and has driven parts of projects such as the Brain Somatic Mosaicism Network. However, a major roadblock in identifying these ele- ments remains as their inherent repetitive nature makes them difficult to place on a genome. In this proposal, we will develop a technology to capture a set of actively moving transposable elements: L1Hs, AluYa5/8, AluYb8/9, and SVAs. These represent the vast majority of active transposable elements and thus will allow us to measure the genetic diversity of polymorphic insertions of these elements. After capture, we will use nanopore long-read sequencing to capture both the entire insertion as well as thousands of bases of surrounding sequence which will allow for accurate mapping of these elements to the genome. We will apply this new technology to a set of three diverse trios that have been well-studied and characterized to allow for follow-up analysis of the effect of polymorphic insertions of transposable elements.

项目摘要 虽然在分析中经常被忽视，但基因组的重复区域及其与疾病的关联正变得越来越重要。 近年来更加明显。人们对这些地区兴趣的复苏，部分原因是新技术的可用性- nologies测序them and accurately准确map地图their其location位置.事实上，转座因子的种类有 在人群中表现出多态性，表明它们在塑造我们的基因组方面持续活跃， 以及它们成为表型的遗传驱动因素的倾向。对于神经系统疾病来说尤其如此， 其中转座因子不仅是多态的，而且在体细胞中活跃地移动， 脑体嵌合网络（Brain Somatic Mosaicism Network）。然而，识别这些电子设备的主要障碍是- 片段仍然存在，因为它们固有的重复性质使它们难以放置在基因组上。在这项提案中， 我们将开发一种技术来捕获一组活跃移动的转座因子：L1 H，L1 Ya 5/8， Yb 8/9和SVAs。这些代表了绝大多数的活性转座因子，因此将允许我们 以测量这些元件的多态性插入的遗传多样性。捕获后，我们将使用纳米孔 长读段测序以捕获整个插入以及周围序列的数千个碱基 这将允许这些元件到基因组的精确映射。我们将把这项新技术应用于 一套三个不同的三重奏，已得到充分研究和特点，以允许后续分析的 转座因子多态性插入的影响。