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）：本申请要求由454序列开发的Roche Genome Sequencer FLX（GS FLX），用于在Johns Hopkins Bloomberg公共卫生学院安置。该仪器产生超过100万个独特的高质量测序读数，平均在十小时的仪器运行时间内长度为350至400个基底。每次仪器运行的总平均收益率为400至500兆瓦。该工具将由一组不同的调查员组使用，该研究人员解决了与当今世界面临的主要疾病流行有关的问题。代表性的研究包括药物使用者和接受预防性抗逆转录病毒治疗的母亲的抗逆转录病毒治疗的主要抗药性。这些研究将评估该技术在指导这些不同环境中初始抗逆转录病毒疗法的有用性。在缺乏传统抗性机制的结核菌中，将研究对抗结核药物抗性的遗传基础。将使用该仪器定义可以或无法完成蚊子传播周期的疟疾寄生虫之间的差异，蚊子对疟疾的存在的先天免疫反应也会定义。通过鉴定酵母基因敲除菌株中补偿性突变的研究可以阐明癌症的生物学，其中许多二次突变在癌细胞系中观察到表型。同样，研究将表征那些在肝细胞癌个体中鉴定出的丙型肝炎病毒变体的不同遗传特征。所有这些研究的共同点都是需要检测大而多样化的基因库中的罕见突变，或者在大型基因组中的突变，这些突变占了不同的表型。在所有需要的情况下，基因组测序仪FLX系统的高通量测序能力都可以解决。该仪器提供的分析工具将有助于拟议的分析，但是该项目还利用了约翰·霍普金斯大学（Johns Hopkins University）专门为基因组分析而建立的生物信息学核心。最终，该仪器将安置在最初用于阵列分析的预先存在的核心设施中，但具有仪器和可用的专业知识来利用高通量测序的能力。