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）：本申请要求罗氏基因组测序仪FLX（GS FLX），由454 Sequencing开发，用于约翰霍普金斯彭博公共卫生学院。该仪器在10小时的仪器运行时间内生成超过100万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率为400至500兆焦耳。该工具将由一组不同的调查人员使用，以解决与当今世界面临的主要疾病流行病有关的问题。有代表性的研究包括关于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原发性抗药性的研究。这些研究将评估该技术在这些不同环境中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的遗传基础。疟疾寄生虫之间的差异，可以或不能完成蚊子的传播周期将使用这一工具，将蚊子？的先天免疫反应的存在疟疾。癌症的生物学可以通过鉴定酵母敲除菌株中的补偿性突变的研究来阐明，其中许多次级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鉴定的那些B型肝炎病毒变异体的独特遗传特征。所有这些研究都有一个共同点，即需要检测大型多样性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，基因组测序仪FLX系统的高通量测序能力都能满足这一需求。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建立的生物信息学核心。最后，该仪器将被安置在一个预先存在的核心设施中，该设施最初是为阵列分析而建立的，但具有利用高通量测序能力的仪器和可用的专业知识。