Massively Parallel High Throughput, Low Cost Sequencing

大规模并行高通量、低成本测序

• 批准号: 7028157
• 负责人: Kenton L Lohman
• 金额: $ 6.28万
• 依托单位: 454 LIFE SCIENCES CORPORATION
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-14 至 2006-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7028157
• 关键词: bioinformatics; biomedical equipment development; genome; high throughput technology; microarray technology; nucleic acid sequence

DESCRIPTION: (provided by applicant) Background: Large-scale genomic sequencing currently requires high cost equipment and is labor intensive. The throughput of conventional sequencing has grown inadequate in fulfilling the escalating demands for genomic sequence. Understanding the intricacies of human genetic organization and how it relates to human health and inheritance, requires genomic-level comparative analyses that cannot currently be performed due to the lack of sequence information. The 454 Corporation has developed a massively parallel, high-throughput sequencing instrument that combines simultaneous sequencing in hundreds of thousands of picoliter-scale reaction wells, with high-powered bioinformatics. The method does not require an exponential scale up in effort or cost, despite exponential increases in genome size. The effort and cost of conventional sequencing scales up proportionately with the size of the genome. The 454 approach will be low cost, and make sequencing large genomes available to a wide variety of laboratories. Specific Aims: In this Program we will (i) Construct a robust double-ended sequencing method that generates short sequences from both ends of each individual fragment (ii) Develop a robust sequence assembly tool appropriate for double-ended sequencing (iii) Prototype the use of our scaled up system, with double-ended sequencing for economical, rapid haplotyping of mammalian organisms. Our Study design incorporates a multi-disciplinary effort across molecular biology, chemistry, engineering, software and bioinformatics groups at 454 Corporation. The molecular biology and sequencing efforts will be lead by the PI, Dr. Kenton L. Lohman. The hardware, fluidics, optics, software and bioinformatics efforts will be lead by co-PI, Dr. Marcel Margulies. We will be taking advantage of current 454 infrastructure, and key personnel. Relevance: There is a growing need across the research, pharmaceutical and clinical communities for low-cost, high throughput genomic sequencing. Comparative genomics, SNP and haplotype analyses have shown tremendous potential to rapidly characterize individual susceptibilities to many classes of chronic and acute diseases and disorders. Current costs of whole genome sequencing can only be borne by large institutions. The cost of automated sample preparation and sequencing, scales up proportionately to the size of the genome being sequenced. The 454 Sequencing system simultaneously analyzes millions of fragments in massively parallel sequencing of mammalian organisms. The use of massively parallel sequencing and bioinformatics analysis creates a low cost, high throughput sequencing system.

描述：（由申请人提供）背景：大规模基因组测序目前需要高成本的设备并且是劳动密集型的。 传统测序的通量已不足以满足对基因组序列不断增长的需求。 了解人类遗传组织的复杂性及其与人类健康和遗传的关系，需要进行基因组水平的比较分析，但由于缺乏序列信息，目前尚无法进行这种分析。 454 Corporation 开发了一种大规模并行、高通量测序仪器，它将数十万皮升规模反应孔中的同步测序与高性能生物信息学相结合。 尽管基因组大小呈指数级增加，但该方法不需要指数级增加工作量或成本。 传统测序的工作量和成本与基因组的大小成比例地增加。 454 方法成本较低，并且可以为各种实验室提供大型基因组测序。 具体目标：在本计划中，我们将 (i) 构建一种强大的双端测序方法，从每个单独片段的两端生成短序列 (ii) 开发适合双端测序的强大序列组装工具 (iii) 对我们的放大系统的使用进行原型设计，通过双端测序对哺乳动物生物体进行经济、快速的单倍型分析。 我们的研究设计融合了 454 Corporation 分子生物学、化学、工程、软件和生物信息学小组的多学科努力。 分子生物学和测序工作将由 PI Kenton L. Lohman 博士领导。 硬件、流体学、光学、软件和生物信息学工作将由联合 PI Marcel Margulies 博士领导。 我们将利用当前的 454 基础设施和关键人员。 相关性：研究、制药和临床界对低成本、高通量基因组测序的需求日益增长。 比较基因组学、SNP 和单倍型分析已显示出快速表征个体对多种慢性和急性疾病和病症的易感性的巨大潜力。 目前全基因组测序的费用只能由大型机构承担。 自动化样品制备和测序的成本与被测序的基因组的大小成比例地增加。 454 测序系统可在哺乳动物生物体的大规模并行测序中同时分析数百万个片段。 大规模并行测序和生物信息学分析的使用创建了低成本、高通量的测序系统。

项目成果

Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing.

• DOI: 10.1186/1471-2164-7-216
• 发表时间: 2006-08-23
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Pinard R;de Winter A;Sarkis GJ;Gerstein MB;Tartaro KR;Plant RN;Egholm M;Rothberg JM;Leamon JH
• 通讯作者: Leamon JH