Large Scale Sequencing at BCM-HGSC

BCM-HGSC 大规模测序

• 批准号: 6739914
• 负责人: RICHARD A GIBBS
• 金额: $ 3037.55万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-11-10 至 2006-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6739914
• 关键词: artificial chromosomes; complementary DNA; computer assisted sequence analysis; computer program /software; computer system design /evaluation; cooperative study; fluid flow; genetic models; genome; nucleic acid sequence

DESCRIPTION (provided by applicant): The Baylor College of Medicine Human Genome Sequencing Center will produce draft sequences of the rhesus macaque and bovine genomes and extract maximal biological information from these data. At the same time the technology for deciphering large genomes will be improved. To do this, shotgun sequencing capabilities will be expanded (to 3.5 million reads/month) while reducing costs (to $0.50/read). A combined approach using both BAC and Whole Genome Shotgun reads will be employed, with the BAC sequencing employing the Clone Array Pooled Shotgun Sequencing strategy that has been developed at the BCM-HGSC. Assembly of the genomes will use the ATLAS genome assembly software, developed for the rat genome project at the BCM-HGSC, which will be enhanced during this project. The draft sequence products will also include 10-15% finished sequence. To achieve this, finishing capacity will be increased through the combination of incremental improvements in existing methods, application of the Genome Wide strategy used in the Drosophila melanogaster project, and a novel procedure using massive numbers of short inexpensive reads. Numerous other developments will occur throughout the BCM-HGSC operation during this project including establishment of a second more cost efficient facility for production sequencing, introduction of 192 plate formats and microfluidics in production sequencing, expansion of annotation capabilities, establishment of a software engineering team, and development of a high performance computing architecture. Augmenting the draft sequence products will be cDNA sequencing to assist in gene modeling.

描述（由申请人提供）：贝勒医学院人类基因组测序中心将生成恒河猴和牛基因组的草图序列，并从这些数据中提取最大的生物信息。 与此同时，破译大基因组的技术也将得到改进。 为此，鸟枪法测序能力将扩大（至每月 350 万次读取），同时降低成本（至每次读取 0.50 美元）。 将采用使用 BAC 和全基因组鸟枪读取的组合方法，其中 BAC 测序采用 BCM-HGSC 开发的克隆阵列池鸟枪测序策略。 基因组组装将使用 ATLAS 基因组组装软件，该软件是为 BCM-HGSC 的大鼠基因组项目开发的，该软件将在该项目期间得到增强。草稿序列产品还将包括 10-15% 的成品序列。 为了实现这一目标，将通过结合现有方法的增量改进、果蝇项目中使用的全基因组策略的应用以及使用大量短的廉价读取的新程序来提高整理能力。在该项目期间，整个 BCM-HGSC 运营过程中将出现许多其他发展，包括建立第二个更具成本效益的生产测序设施、在生产测序中引入 192 板格式和微流体、扩展注释功能、建立软件工程团队、以及高性能计算架构的开发。 cDNA 测序将增强草图序列产品，以协助基因建模。