Genome Sequencer FLX Instrument

描述(由申请人提供)：本资助申请是为罗氏基因组测序仪(GS)FLX及其专用软件应用程序所需的GS FLX计算机集群申请资金。在一夜之间，该设备可以在400个碱基对的平均读取长度下产生100多万个序列读取，在第400个碱基对位置的单碱基读取准确率为99.99%，产生超过400,000个高质量的序列。然后通过嵌入的GS FLX软件对输出进行分析，以生成仅50 GB的可管理数据文件。该仪器的长读数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。这一应用程序中的元基因组研究将描述广泛研究人群(肺炎或囊性纤维化儿童或感染隐孢子虫的儿童、骨髓移植受者、耐药细菌患者、产志贺毒素大肠杆菌携带者、感染艾滋病毒和丙型肝炎的药物使用者以及炎症性肠道疾病患者)中的肠道微生物区系，只能使用GS FLX系统完成。该平台对整个原核生物突变基因组进行重新测序的能力足以识别小RNA，在复制中解决新的终点，并识别任何其他意想不到的基因组重排，这一能力将用于霍乱弧菌、肺炎链球菌和嗜肺军团菌等感染性病原体的研究。心脏疾病易感性的遗传标记、G蛋白偶联受体变异与肥胖的关联、肺血管疾病的遗传危险因素、头面部骨骼和牙齿发育与再生的遗传调控以及癌症组织中内源性逆转录病毒的寻找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艾滋病毒测序，以评估艾滋病毒耐药性突变和与长期非进展相关的HIV-1包膜蛋白区域。这些设备将存放在先前存在的核心设施中，已经制定了管理计划，塔夫茨医疗中心和塔夫茨大学医学院都承诺提供机构支持。

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.