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)

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 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历史最悠久的实验室，成立于 1990 年代中期，旨在为参与分子生物学技术研究的 MSM 研究人员提供 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析荧光标记的 DNA。 该设施围绕 ABI 3130xl 基因分析仪（16 毛细管）和用于 DNA 序列分析的相关软件构建。 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先进的 DNA 片段（微卫星）分析。测序仪的软件选项允许对患者样本中的多态性 (SNP) 进行计数，该服务可与人类基因分型实验室提供的 SNP 发现结合使用。 DNA测序实验室还拥有可供用户使用的DNA和蛋白质序列分析软件。该实验室还拥有一个暗室，其中配备了用于冲洗 X 射线胶片的自动胶片处理器和用于细菌培养物生长的大容量摇床培养箱，位于暗室附近。 人类基因分型实验室 - 宋青，负责人 分子遗传学核心设施协助研究人员将基因组技术应用于基于人群的遗传研究。该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。核心假设是，健康差异部分与影响常见疾病易感性的关键基因中种族特异性 DNA 变异有关。莫尔豪斯医学院长期以来一直对种族差异研究感兴趣，并且长期致力于向服务不足的少数族裔群体进行社区外展活动。因此，MSM人类基因组核心实验室的主要目标是增强这些样本群体的研究能力，并基于尖端基因组技术将我们的研究提升到分子遗传学水平。我们目前提供新型SNP发现和SNP基因分型服务、生物信息学以及遗传研究设计的一般咨询服务。 基因表达实验室 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，我们将开始将全基因组方法整合到临床问题中，进行探索性研究，在临床上使用微阵列来发现生物标志物；生物标志物足迹的开发可以为靶向治疗带来重要的临床益处。我们将努力让教师意识到未来临床应用的可能性。 我们的总体目标是利用发现生物标志物作为个体化治疗中转化研究和临床开发之间的牢固联系。今年我们有必要对现有设备进行升级，以适应即将推出的新微阵列。 MSM 基因表达实验室的基本目标是提供任何特定时间细胞、组织或器官中表达的基因的广泛但有限的概况。 MSM 研究人员的决定性好处将是加速研究进展并为治疗靶点的识别做出贡献。微阵列技术起源于 20 世纪 90 年代中期，其数据是通过检查一些特定症状而产生的。然而，该技术现在几乎适用于所有新的复杂疾病。 2001 年，MSM 基于安捷伦技术建立了功能基因组学核心实验室，这些疾病研究的遗传学方法开启了新一波的研究浪潮。目前，这些技术用于微生物基础研究以及人类疾病状态的调查。基因芯片技术的决定性好处来自于一次实验可以产生的大量相关数据，从而有望以不可估量的速度加速单个研究项目的进展。 1) TechnoloQV 资源： 安捷伦 2010 生物分析仪 安捷伦扫描微阵列 安捷伦 HP 捆绑工作站 生物分析计算机和相关软​​件 2）核心实验室人员： 米歇尔·利安德 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，旨在为基础、转化和临床研究的研究人员提供企业级生物信息学软件解决方案。在 MSM，我们共同开发了计算生物学，以在微阵列技术不断进步的同时实现这一目标。因此，位于微阵列核心实验室附近的生物信息学套件有助于分析从多平台微阵列（Agilent、Affymetrix 等）收集的基因表达数据。此外，生物信息学实验室人员提供基因表达相关的分析和咨询以及SNP数据分析。生物信息学分析包括但不限于遗传生物标志物的鉴定和有形的诊断应用。 1）技术资源： 主要设备主要部件 1. 戴尔存储服务 1. Gene Sifter 2. HP- 工作站 2. Spotfire 3. 彩色打印机 3 Rosetta Luminator 4. 25台服务器计算机集群 4. 匠心精神 5. Rosetta 应用服务器 5. Silicon Genetics 6. GeneSpring 应用服务器 6. Affymetrix 7. Spotfire 和 Genesifter 7. 其他。软件包 8. 途径 4 9. 数组统计 2) 核心实验室人员 胡星 服务收费： DNA测序实验室 服务成本 DNA 测序：6.00 美元/测序反应 (MSM) $8.00 /反应（非 MSM） 大用户测序折扣 5.00 美元/反应 (MSM) （完整的 96 孔板）每次反应 6.00 美元（非 MSM）。 DNA 片段分析：每个样本 1.50 美元 (MSM) 每个样品 2.00 美元（非 MSM） 胶片冲洗：冲洗机免费使用 摇床-培养箱：使用培养箱免费 人类基因分型实验室 我们刚刚根据从埃默里大学和田纳西大学获得的信息制定了服务收费政策和价目表。然而，由于这种遗传变异核心的性质，它更多的是项目支持核心而不是基于样本的服务；我们在退款方面仍处于开发阶段。在此阶段，我们为许多研究人员的研究设计、提案制定和资助申请提供了支持。这些用户包括，博士。布拉德福德、福尔曼、孟和王。 基因表达实验室 我们为核心实验室提供的服务制定了具有竞争力的价格。定制载玻片需要 4,000.00 美元的设置费用（一次），加上批量载玻片，每张载玻片的成本从 400.00 美元到 800.00 美元不等。注意：定制载玻片也可以由研究者或安捷伦出售，作为支付成本的一种方式。该实验室将与研究人员合作，选择适合他们需求的技术。 微阵列服务成本 幻灯片 - 非人类 $760.00 幻灯片 - 人体高密度 $850.00 幻灯片 所有其他 $700.00 幻灯片习俗各不相同 其他服务费用 RNA 储存解决方案 5.00 美元/管 组织/器官的采集 $30.00/小时 RNA 分离细胞 $30.00 一个 RNA 分离组织 45.00 美元每张 RNA 质量检查/报告 $30.00 免费数据报告/样品 培训：研讨会、实验室可用性； $60.00/小时 包括以上项目加上人工 生物信息学实验室 生物信息学服务 60 美元/小时（咨询/培训）