GENE PROFILING

基因分析

• 批准号: 7959154
• 负责人: WILLIAM W ROTH
• 金额: $ 30.12万
• 依托单位: MOREHOUSE SCHOOL OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-01 至 2010-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7959154
• 关键词: Arts; Back; Basic Science; Bioinformatics; Biological Markers; Biomedical Research; Blood capillaries; Capillary Electrophoresis; Cell Separation; Cells; Charge; Clinic; Clinical; Clinical Research; Clinical Trials; Color; Community Outreach; Complex; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Computer software; Computers; Consultations; Core Facility; Custom; DNA; DNA Sequence; DNA Sequence Analysis; Data; Data Reporting; Development; Diagnostic; Disease; Educational workshop; Equipment; Ethnic Origin; Faculty; Film; Funding; Future; Gene Chips; Gene Expression; Genes; Genetic; Genetic Polymorphism; Genetic Research; Genetic Variation; Genome; Genomics; Genotype; Goals; Grant; Growth; Hour; Human; Human Genome; Human Resources; Incubators; Individual; Institution; Investigation; Label; Laboratories; Link; Microarray Analysis; Microsatellite Repeats; Molecular Biology Techniques; Molecular Genetics; Nature; Organ; Pathway interactions; Patients; Policies; Population; Predisposition; Price; Process; Protein Sequence Analysis; RNA; Reaction; Reporting; Research; Research Design; Research Personnel; Research Project Grants; Resources; Sampling; Science; Services; Silicon; Slide; Solutions; Source; Staging; Strategic Planning; Syndrome; Techniques; Technology; Tennessee; Time; Tissue Banks; Tissues; Training; Translational Research; Tube; Underrepresented Minority; United States National Institutes of Health; Universities; Variant; Work; X-Ray Film; base; capillary; clinical application; cohort; cost; density; discount; functional genomics; health disparity; human disease; improved; instrumentation; interest; medical schools; microorganism; novel; population based; price lists; programs; research study; therapeutic target

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. DNA Sequencing Laboratory  Dr. William Roth, Leader The DNA Sequencing laboratory is the longest-established lab in the Gene Profiling Core, having been established in the mid-1990's to provide DNA sequence analysis to MSM investigators involved in research utilizing molecular biology techniques. The lab uses capillary electrophoresis sequencing technology developed by Applied Biosystems (ABI) to resolve fluorescently-labeled DNA. The facility is built around the ABI 3130xl Gene Analyzer (16-capillary) and associated software for DNA sequence analysis. Recent upgrades to instrumentation and software enable the lab to offer state-of the-art DNA fragment (microsatellite) analysis to research users. Software options for the sequencer allow enumeration of polymorphisms (SNPs) in patient samples, a service which can be used in conjunction with SNP discovery offered in the Human Genotyping Lab. The DNA Sequencing lab also has DNA and protein sequence analysis software which is available to users. The lab also maintains a darkroom with an automated film processor for developing X-ray films and a large capacity shaker-incubator for growth of bacterial cultures, located adjacent to the darkroom. Human Genotyping Lab - Qing Song, Leader The Molecular Genetics Core Facility assists investigators to apply the genomic technologies to population-based genetic research. The strategic plan is to create a link between basic science, clinical investigation and population-based research by integrating genomic sciences into our research program. The central hypothesis is that health disparities are related in part to ethnicity-specific DNA variants in critical genes that influence the susceptibility to common diseases. Morehouse School of Medicine has a long-standing interest on the studies of ethnic disparities and a longstanding strength on community outreach to underserved minority populations. Accordingly, the major objective of the MSM Human Genome Core Laboratory is to enhance the research capacity on these sample cohorts and upgrade our research to the molecular genetics level based on cutting-edge genomic technologies. We currently provide service on the novel SNP discovery and SNP genotyping service, bioinformatics and general consultation on genetic study design. Gene Expression Lab  Dr. Nerimiah Emmett, Leader The Genomic Core Facility continues to offer an integrated Genomic-based approach for basic research problems and clinical applications. With the establishment of CTSIA we will begin to integrated whole genome approaches to clinical problems for exploratory studies using micro array in the clinic for biomarker discovery; the development of biomarker footprints can have important clinical benefits for targeted therapeutics. We will push to make the faculty aware of the possibilities in future clinical applications. Our overall goal is to use discovery biomarkers as strong links between translational research and clinical development in individualized treatments. Upgrades to our existing equipment will be necessary this year to accommodate the new microarrays that will be available. The fundamental goal of the Gene Expression Laboratory at MSM is to provide an extensive, yet finite profile of the genes expressed in cells, tissues or organs at any given time. The defining benefit to MSM investigators will be to accelerated the research progress and contribute with respect to the identification of therapeutic targets. Micro array technology had its origin in the mid 1990's, with data produced from examination of a few specific syndromes; however, the technology is now applicable to virtually all new complex diseases. These genetic approaches to disease study began a new wave of investigation at MSM in 2001 with establishment of the Functional Genomics Core Laboratory based on the Agilent Technology. Currently, these techniques are used for basic research on microorganisms as well as the investigation of human disease states. The defining benefit of gene chip technology is derived from the enormous amount of relevant data that can be generated from a single experiment, thereby promising to accelerate the progress of individual research projects at an immeasurable rate. 1) TechnoloQV Resources: Agilent 2010 Bioanalyzer Agilent Scanner Micro array Agilent HP Bundle Workstation Bioanalyzer computers and associated software 2) Core Lab Personnel: Michelle Leander Bioinformatics Lab  Dr. Leonard Anderson, Leader The bioinformatics suite was established at MSM in 2001 in order to provide enterprise level bioinformatics software solutions for investigators in basic, translational, and clinical research. At MSM we have co-developed computational biology to accomplish this objective at the same time as microarray technology has improved. Thus, the bioinformatics suite, located adjacent to the micro array core laboratory, facilitates analysis of gene expression data gathered from multiplatform microarrays (Agilent, Affymetrix, etc). In addition, Bioinformatics Lab personnel provide analysis and consultation related to gene expression and analysis of SNP data. Bioinformatics analysis includes, but is not limited to identification of genetic biomarkers and tangible diagnostic applications. 1) Technology Resources: Major Equipment Principal Components 1. Dell Storage Services 1. Gene Sifter 2. HP- Work Stations 2. Spotfire 3. Color Printers 3 Rosetta Luminator 4. 25 Server Computer Cluster 4. Ingenuity 5. Rosetta Application Server 5. Silicon Genetics 6. GeneSpring Application server 6. Affymetrix 7. Spotfire and Genesifter 7. Misc. Software Packages 8. Pathways 4 9. Array STAT 2) Core Lab Personnel Xing Hu Service Charges: DNA Sequencing Lab Service Cost DNA Sequencing: $6.00 /sequencing reaction (MSM) $8.00 /reaction (non-MSM) Large-user sequencing discount $5.00/reaction (MSM) (full 96-well plate) $6.00/reaction (non-MSM). DNA Fragment Analysis: $1.50 per sample (MSM) $2.00 per sample (non-MSM) Film processing: no charge for use of the processor Shaker-Incubator: no charge for use of the incubator Human Genotyping Lab We have just developed a service charge policy and price list, based on the information obtained from Emory University and University of Tennessee. However, due to the nature of this genetic variation core, it is more project-support core rather than a sample-based service; we are still in the developing stage on charging-back. At this stage, we have supported a number of researchers in their study design, proposal development, and grant submission. These users include, Drs. Bradford, Foreman, Meng, and Wang. Gene Expression Lab We have established competitive pricing for services offered by the Core Laboratory. Custom slides require at $4,000.00 set-up charge (one time) plus batches of slides at a cost which varies from $400.00 - $800.00 per slide. Note: customized slides can also be sold either by the investigator or by Agilent as a means to cover cost. The lab will work investigators to select appropriate technology for their needs. Micro array Services Cost Slides - Non Human $760.00 Slides - Human High Density $850.00 Slides  All Others $700.00 Slides  Customs Varies Other Services Cost RNA Storage Solutions $5.00/tube Collection of Tissues/Organs $30.00/hour RNA Isolation  cells $30.00 ea RNA Isolation  Tissues $45.00 ea RNA Quality checks/reports $30.00 DATA Reports/Samples FREE Training: Workshops, Lab Availability; $60.00/hour Inclusive of items above plus labor Bioinformatics Lab Bioinformatics service $60 / hour (consultation/training)

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 DNA测序实验室William Roth博士，负责人 DNA测序实验室是基因分析核心中最长的实验室，该实验室已在1990年代中期建立，目的是向参与研究分子生物学技术研究的MSM研究者提供DNA序列分析。 该实验室使用Applied Biosystems（ABI）开发的毛细管电泳测序技术来解决荧光标记的DNA。 该设施围绕ABI 3130XL基因分析仪（16毛细血管）和相关软件，用于DNA序列分析。 最近对仪器和软件的升级使实验室能够为研究用户提供最新的DNA片段（微卫星）分析。音序器的软件选项允许患者样本中的多态性（SNP）列举，该服务可与人类基因分型实验室中提供的SNP发现一起使用。 DNA测序实验室还具有可供用户使用的DNA和蛋白质序列分析软件。该实验室还维护着一个带有自动胶片处理器的暗室，用于开发X射线胶片和大量容量振动筛，以供细菌培养物生长，该细菌培养物的生长位于黑室附近。 人类基因分型实验室 - 清楚，领导者 分子遗传学核心设施有助于研究人员将基因组技术应用于基于人群的遗传研究。战略计划是通过将基因组科学整合到我们的研究计划中，在基础科学，临床研究和基于人群的研究之间建立联系。中心假设是，健康差异部分与关键基因的种族特异性DNA变异有关，这些基因影响了对常见疾病的易感性。莫尔豪斯（Morehouse）医学学院对种族差异的研究和对少数人服务不足的少数民族的长期实力对研究产生了长期的兴趣。因此，MSM人类基因组核心实验室的主要目的是提高这些样本队列的研究能力，并将我们的研究升级到基于尖端基因组技术的分子遗传学水平。我们目前提供有关新型SNP发现和SNP基因分型服务，生物信息学和遗传研究设计一般咨询的服务。 Gene Expression Lab Nerimiah Emmett博士，负责人 基因组核心设施继续为基础研究问题和临床应用提供基于基因组的综合方法。随着CTSIA的建立，我们将开始将整个基因组方法整合到临床问题上，以使用诊所中的微阵列进行探索性研究，以进行生物标志物发现；生物标志物足迹的开发可以为有针对性的治疗剂带来重要的临床益处。我们将努力使教师意识到将来的临床应用中的可能性。 我们的总体目标是将发现生物标志物用作个性疗法中转化研究与临床发展之间的牢固联系。今年将需要升级到我们现有的设备，以适应可用的新微阵列。 MSM基因表达实验室的基本目标是在任何给定时间提供在细胞，组织或器官中表达的基因的广泛但有限的概况。 MSM研究人员的定义好处将是加速研究进度，并在识别治疗靶点方面做出贡献。微型阵列技术起源于1990年代中期，并通过检查一些特定综合症而产生的数据。但是，该技术现在适用于几乎所有新的复杂疾病。这些疾病研究的遗传方法于2001年开始在MSM进行新的研究，并基于安捷伦技术建立了功能性基因组学核心实验室。目前，这些技术用于微生物以及人类疾病状态的研究。基因芯片技术的定义好处是从可以从单个实验中产生的大量相关数据得出的，从而有望以不可估量的速度加速单个研究项目的进度。 1）TechnoloQV资源： Agilent 2010 Bioanalyzer 安捷伦扫描仪微阵列 安捷伦HP捆绑工作站 生物分析仪计算机和相关软​​件 2）核心实验室人员： 米歇尔·莱恩德（Michelle Leander） 生物信息学实验室Leonard Anderson博士，负责人 生物信息学套件于2001年在MSM建立，以便为研究人员提供基本，转化和临床研究的研究人员的企业级生物信息学软件解决方案。在MSM，我们已经共同开发了计算生物学，可以在微阵列技术改进的同时完成这一目标。因此，位于微阵列核心实验室附近的生物信息学套件促进了从多平台微阵列（Agilent，Affymetrix等）收集的基因表达数据的分析。此外，生物信息学实验室人员提供了与SNP数据的基因表达和分析有关的分析和咨询。生物信息学分析包括但不限于识别遗传生物标志物和有形诊断应用。 1）技术资源： 主要设备主要组件 1。DellStorage Services 1。基因筛 2。HP-工作站2。Spotfire 3。颜色打印机3 Rosetta Luminator 4。25服务器计算机群集4。 5。Rosetta应用程序服务器5。硅遗传学 6。基因弹簧应用程序服务器6。affymetrix 7. Spotfire和Genesifter7。Misc。软件包 8。途径4 9。数组统计 2）核心实验室人员 Xing Hu 服务费： DNA测序实验室 服务成本 DNA测序：$ 6.00 /测序反应（MSM） $ 8.00 /反应（非MSM） 大用户测序折扣$ 5.00/反应（MSM） （完整的96孔板）$ 6.00/反应（非MSM）。 DNA碎片分析：每样本$ 1.50（MSM） 每个样品$ 2.00（非MSM） 电影处理：不使用处理器 振荡器调查器：使用孵化器不收取 人类基因分型实验室 根据埃默里大学和田纳西大学获得的信息，我们刚刚制定了服务收费政策和价格表。但是，由于这种遗传变异核心的性质，它是项目支持的核心，而不是基于样本的服务。我们仍处于充电阶段的发展阶段。在此阶段，我们支持了许多研究人员的研究设计，提案开发和赠款提交。这些用户包括Drs。布拉德福德，工头，孟和王。 基因表达实验室 我们已经为核心实验室提供的服务建立了竞争性定价。自定义幻灯片需要$ 4,000.00的设置费（一次）加上批次幻灯片，价格从每幻灯片$ 400.00- $ 800.00不等。注意：调查员或安捷伦（Agilent）也可以出售定制的幻灯片，以弥补成本。该实验室将为调查人员提供为他们的需求选择适当的技术。 微阵列服务费用 幻灯片 - 非人类$ 760.00 幻灯片 - 人类高密度$ 850.00 滑动所有其他$ 700.00 幻灯片习俗各不相同 其他服务成本 RNA存储解决方案$ 5.00/管 纸巾/器官收集$ 30.00/小时 RNA隔离单元$ 30.00 EA RNA隔离组织$ 45.00 EA RNA质量检查/报告$ 30.00 数据报告/样品免费 培训：讲习班，实验室可用性； $ 60.00/小时 包括上面的物品加人工 生物信息学实验室 生物信息学服务$ 60 /小时（咨询 /培训）