Massively Parallel High Throughput, Low Cost Sequencing

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。 常规测序的通量已变得不足以满足对基因组序列的不断增长的需求。 了解人类遗传组织的复杂性以及它与人类健康和遗传的关系，需要基因组水平的比较分析，由于缺乏序列信息，目前无法进行。 454公司开发了一种大规模并行、高通量测序仪器，该仪器将数十万皮升规模反应威尔斯孔中的同时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，但该方法不需要在努力或成本上呈指数级增加。 常规测序的工作量和成本随着基因组的大小成比例地增加。 454方法将是低成本的，并使测序大基因组可用于各种实验室。 具体目标：在这个项目中，我们将（i）构建一个强大的双端测序方法，从每个单独片段的两端产生短序列（ii）开发一个强大的序列组装工具，适用于双端测序（iii）原型使用我们的规模扩大的系统，双端测序经济，快速单倍型的哺乳动物生物体。 我们的研究设计融合了454 Corporation的分子生物学、化学、工程、软件和生物信息学团队的多学科努力。 分子生物学和测序工作将由主要研究者Dr.洛曼 硬件，流体，光学，软件和生物信息学工作将由共同PI Marcel Margulies博士领导。 我们将利用现有的454基础设施和关键人员。 相关性：研究、制药和临床领域对低成本、高通量基因组测序的需求日益增长。 比较基因组学、SNP和单倍型分析已经显示出快速表征个体对许多类别的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成本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产生了低成本、高通量测序系统。

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.