Drosophila Population Genomics

果蝇群体基因组学

• 批准号: 8068985
• 负责人: CHARLES HUNT LANGLEY
• 金额: $ 30万
• 依托单位: UNIVERSITY OF CALIFORNIA AT DAVIS
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-07 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8068985
• 关键词: Address; Advanced Development; Affect; Africa; Animal Model; Animals; Asia; Asians; Attention; Automobile Driving; Biomedical Research; Communities; Complex; Computer software; DNA Resequencing; DNA Sequence; Data; Detection; Development; Drosophila genome; Drosophila genus; Drosophila melanogaster; Environment; Europe; European; Exhibits; Foundations; Genes; Genetic; Genetic Polymorphism; Genetic Research; Genome; Genomics; Genotype; Goals; Human; Human Biology; Human Genome; Individual; Investigation; Laboratories; Maps; Medicine; Methodology; Methods; Phenotype; Play; Population; Population Genetics; Process; Production; Reading; Research; Research Project Grants; Resources; Role; Sampling; Sequence Analysis; Shapes; Solid; Statistical Models; Strategic Planning; Structure; Supercomputing; System; Talents; Technology; Time; Variant; Vision; base; clinical practice; design; disorder risk; genome sequencing; high end computer; insight; instrument; programs; public health relevance

DESCRIPTION (provided by applicant): The vision of routine whole genome resequencing for human genomics research and ultimately medicine is at the same time filled with immeasurable promise and daunting technical and conceptual challenges. The model organism Drosophila melanogaster has and continues to play a vibrant critical role in the advancement of methods and ideas used to understand variation in the structure and function of animal genomes. Recently released high-throughput sequencing platforms offer the first step on the path to the $1000 (or even $100) human genome. The early applications of these technologies already focus our attention on the enormous computational and analytic challenges of moving such vast genomic sequencing capacity to every laboratory. This proposal is an attempt to directly and creatively address these challenges by integrating the new high-throughput sequencing platforms with cutting-edge, small-footprint supercomputing to provide a large population sample (>1000) of sequenced genomes and their associated stocks to the imaginative and energetic Drosophila research community. To create this unique resource an efficient cluster of three high-throughput sequencing instruments will be integrated with four small-footprint, modular (FPGA-based) high performance computers that can support both the development of advance methods and the production of high quality syntenic assemblies. The availability of such large numbers of carefully sampled and sequenced Drosophila genomes will stimulate the population genetics research community to begin to address the fundamental mechanistic forces that shape variation among individual at a truly genomic scale. PUBLIC HEALTH RELEVANCE The goal of this project is to advance the technology and analytic methods for understanding genomic variation in populations by integrating benchtop supercomputing with ultra high- throughput resequencing to characterize a large sample of genomes of the fruitfly, Drosophila melanogaster. The envisioned rapid advance in the model organism system will provide essential ideas and talent to human population genomics research.

描述（由申请人提供）：人类基因组学研究和最终医学的常规全基因组重测序的愿景同时充满了不可估量的前景和令人畏惧的技术和概念挑战。模式生物果蝇在用于了解动物基因组结构和功能变异的方法和思想的进步中已经并将继续发挥着充满活力的关键作用。最近发布的高通量测序平台为通向 1000 美元（甚至 100 美元）人类基因组之路迈出了第一步。这些技术的早期应用已经将我们的注意力集中在将如此巨大的基因组测序能力转移到每个实验室所面临的巨大计算和分析挑战上。该提案试图通过将新的高通量测序平台与尖端的小型超级计算相结合，直接、创造性地应对这些挑战，为富有想象力的人们提供大量的已测序基因组样本（> 1000）及其相关库存。和充满活力的果蝇研究社区。为了创建这种独特的资源，由三台高通量测序仪器组成的高效集群将与四台小型模块化（基于 FPGA）高性能计算机集成，这些计算机可以支持先进方法的开发和高质量同线组件的生产。如此大量的经过仔细采样和测序的果蝇基因组的可用性将刺激群体遗传学研究界开始解决在真正的基因组规模上塑造个体变异的基本机制力量。公共健康相关性 该项目的目标是通过将台式超级计算与超高通量重测序相结合来表征果蝇（Drosophila melanogaster）的大量基因组样本，从而推进了解群体基因组变异的技术和分析方法。模型生物系统的快速发展将为人类基因组学研究提供重要的思想和人才。