Genome Sequencer FLX Instrument

基因组测序仪FLX仪器

• 批准号: 7795343
• 负责人: Anne Virginia Kane
• 金额: $ 49.35万
• 依托单位: TUFTS MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-06-10 至 2012-06-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7795343
• 关键词: Antibiotic Resistance; Bacteria; Base Pairing; Bone Marrow Transplantation; Child; Computer software; Core Facility; Cryptosporidium; Cystic Fibrosis; DNA Sequence Rearrangement; Development; Disease susceptibility; Drug user; Endogenous Retroviruses; Equipment; Escherichia coli EHEC; Funding; G-Protein-Coupled Receptors; Gene Expression Profile; Genetic; Genetic Markers; Genome; Grant; HIV; HIV drug resistance; HIV-1; Heart Diseases; Hepatitis C; Housing; Infectious Agent; Inflammatory Bowel Diseases; Intestines; Legionella pneumophila; Length; Lung; Malignant Neoplasms; Medical center; Metagenomics; Natural regeneration; Obesity; Output; Patients; Pneumonia; Population Study; Positioning Attribute; Prokaryotic Cells; Reading; Regulation; Research; Research Personnel; Running; Sequence Analysis; Small RNA; Streptococcus pneumoniae; System; Tissues; Tooth structure; Transplant Recipients; Universities; Variant; Vascular Diseases; Vibrio cholerae; base; computer cluster; craniofacial; env Gene Products; genetic risk factor; instrument; interest; medical schools; mutant; novel; resistance mutation; skeletal

DESCRIPTION (provided by applicant): This grant submission is to request funding for the Roche Genome Sequencer (GS) FLX and the GS FLX Computer Cluster required for its dedicated software applications. In an overnight run, this equipment can generate over a million sequence reads at an average read-length of 400 base pairs with a single-base read accuracy of >99.99% at the 400th base pair position, yielding over 400,000 high quality sequences. The output is then analyzed by imbedded GS FLX software to generate manageable datafiles of only 50GB. The instrument's long read length capability is uniquely suited to several applications of particular interest to investigators at Tufts Medical Center and Tufts University School of Medicine. The metagenomic studies in this application which will characterize the intestinal microbiota in a wide range of study populations (children with pneumonia or cystic fibrosis or infected with Cryptosporidium, recipients of bone marrow transplants, patients colonized with antibiotic resistant bacteria, carriers of Shiga-toxin producing E. coli, HIV and Hepatitis C infected drug users, and patients with inflammatory bowel disease) can only be done using the GS FLX system. The platform's ability to re-sequence entire prokaryote mutant genomes at a read length sufficient to identify small RNAs, resolve the novel endpoints in duplications, and identify any other unanticipated genome rearrangements will be used in studies of the infectious agents Vibrio cholera, Streptococcus pneumoniae and Legionella pneumophila. Research on genetic markers of cardiac disease susceptibility, the association of G protein-coupled receptor variants with obesity, genetic risk factors for pulmonary vascular disease and genetic regulation of craniofacial skeletal and tooth development and regeneration as well as a search for endogenous retroviruses in cancer tissue will depend on its unique transcriptome sequencing and analysis capability. In addition, deep sequencing will be used to achieve full length HIV sequencing to assess HIV drug resistance mutations and regions of HIV-1 envelope protein related to long term non-progression. The equipment will be housed in a pre-existing Core facility, a plan for its management has been developed, and institutional support has been pledged by both Tufts Medical Center and Tufts University School of Medicine.

描述（由申请人提供）：此拨款申请是为了申请罗氏基因组测序仪（GS）FLX和GS FLX计算机集群的专用软件应用程序所需的资金。在过夜运行中，该设备可以以400个碱基对的平均读取长度生成超过一百万个序列读取，其中在第400个碱基对位置处的单碱基读取准确度>99.99%，产生超过400，000个高质量序列。然后通过嵌入式GS FLX软件分析输出，以生成仅50 GB的可管理文件。该仪器的长读长能力特别适合塔夫茨医学中心和塔夫茨大学医学院的研究人员特别感兴趣的几种应用。本申请中的宏基因组学研究将表征广泛研究人群（患有肺炎或囊性纤维化或感染隐孢子虫的儿童、骨髓移植的接受者、抗生素抗性细菌定殖的患者、产志贺毒素的大肠杆菌的携带者）中的肠道微生物群。大肠杆菌、HIV和丙型肝炎感染的吸毒者以及患有炎症性肠病的患者）只能使用GS FLX系统进行。该平台能够以足以识别小RNA的读取长度对整个原核生物突变基因组进行重新测序，解析重复中的新终点，并识别任何其他未预料到的基因组重排，这将用于感染性病原体霍乱弧菌，肺炎链球菌和嗜肺军团菌的研究。对心脏病易感性的遗传标记、G蛋白偶联受体变体与肥胖的关联、肺血管疾病的遗传风险因素、颅面骨骼和牙齿发育和再生的遗传调控以及对癌组织中内源性逆转录病毒的研究将取决于其独特的转录组测序和分析能力。此外，深度测序将用于实现全长HIV测序，以评估HIV耐药突变和与长期非进展相关的HIV-1包膜蛋白区域。这些设备将被安置在一个预先存在的核心设施中，其管理计划已经制定，塔夫茨医学中心和塔夫茨大学医学院都承诺提供机构支持。