Roche 454 Genome Sequencer FLX

罗氏 454 基因组测序仪 FLX

• 批准号: 7794303
• 负责人: Richard B. Markham
• 金额: $ 43.99万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7794303
• 关键词: Accounting; Address; Antiretroviral resistance; Antitubercular Agents; Bacillus (bacterium); Base Pairing; Bioinformatics; Cancer Biology; Cancer cell line; Core Facility; Culicidae; Disease; Drug user; Epidemic; Gene Pool; Genetic; Genome; HIV; Hepatitis B Virus; Hour; Housing; Immune response; Individual; Infant; Knock-out; Length; Malaria; Mothers; Mutation; Parasites; Phenotype; Primary carcinoma of the liver cells; Public Health Schools; Reading; Request for Applications; Research Personnel; Resistance; Running; System; Technology; Time; Universities; Variant; Yeasts; analytical tool; antiretroviral therapy; base; instrument; instrumentation; prophylactic; resistance mechanism; transmission process

DESCRIPTION (provided by applicant): This application requests a Roche Genome Sequencer FLX (GS FLX), developed by 454 Sequencing for placement in the Johns Hopkins Bloomberg School of Public Health. This instrument generates over one million unique high quality sequencing reads with an average of 350 to 400 bases pairs in length within a ten hour instrument run time. The total average yield per instrument run is 400 to 500 megabases. The instrument will be used by a diverse group of investigators addressing questions related to the major disease epidemics confronting the world today. Representative studies include those of primary resistance to antiretroviral therapy for HIV among drug users and among infants born to mothers receiving prophylactic antiretroviral therapy. These studies will evaluate the usefulness of this technology for guiding initial antiretroviral therapy in those distinct settings. The genetic basis for resistance to anti-tuberculosis agents will be studied among tubercle bacilli lacking the traditional resistance mechanisms. Differences among malaria parasites that can or cannot complete the transmission cycle in mosquitoes will be defined using this instrument, as will the mosquito?s innate immune response to the presence of malaria. The biology of cancer may be elucidated by studies identifying compensatory mutations in yeast knockout strains, with many secondary mutations yielding phenotypes observed in cancer cell lines. Similarly studies will characterize distinct genetic features of those hepatitis B virus variants identified in individuals with hepatocellular carcinoma. All of these studies have in common the need to detect either rare mutations in a large and diverse gene pool or mutations in a large genome that account for a distinct phenotype. In all cases that need is addressed by the high throughput sequencing capability of the Genome Sequencer FLX system. Analytical tools provided with the instrument will aid in the proposed analyses, but this project also takes advantage of a bioinformatics core established specifically for purposes of genome analysis at Johns Hopkins University. Finally the instrument will be housed in a pre-existing core facility originally established for array analysis but with the instrumentation and available expertise to exploit the capabilities of high throughput sequencing.

描述（由申请人提供）：本申请要求使用 454 Sequencing 开发的罗氏基因组测序仪 FLX (GS FLX)，用于约翰霍普金斯大学彭博公共卫生学院。该仪器在十小时仪器运行时间内生成超过一百万个独特的高质量测序读数，平均长度为 350 至 400 个碱基对。每次仪器运行的总平均产量为 400 至 500 兆碱基。该工具将由不同的研究小组使用，以解决与当今世界面临的主要疾病流行相关的问题。代表性研究包括吸毒者和接受预防性抗逆转录病毒治疗的母亲所生婴儿对艾滋病毒抗逆转录病毒治疗的主要耐药性的研究。这些研究将评估该技术在这些不同环境下指导初始抗逆转录病毒治疗的有用性。将在缺乏传统耐药机制的结核杆菌中研究抗结核药物耐药性的遗传基础。使用该仪器将确定能够或不能完成蚊子传播周期的疟疾寄生虫之间的差异，以及蚊子对疟疾存在的先天免疫反应。癌症的生物学可以通过鉴定酵母敲除菌株中补偿性突变的研究来阐明，许多二次突变产生在癌细胞系中观察到的表型。类似的研究将描述在肝细胞癌患者中发现的乙型肝炎病毒变体的独特遗传特征。所有这些研究的共同点是需要检测大型且多样化的基因库中的罕见突变或大型基因组中导致不同表型的突变。在所有情况下，Genome Sequencer FLX 系统的高通量测序能力都可以满足这一需求。该仪器提供的分析工具将有助于拟议的分析，但该项目还利用了约翰霍普金斯大学专门为基因组分析目的而建立的生物信息学核心。最后，该仪器将被安置在最初为阵列分析而建立的现有核心设施中，但配备了仪器和可用的专业知识来利用高通量测序的能力。