CAP - Consortium to Alleviate PTSD- STVHCS Biomarkers & Genomics Core

生物标志物与基因组学核心 生物标记物和基因组学核心的主要目标是：(1)支持强星的努力- 生物标志物或基因组成分的CAP研究涉及收集和分析生物和 生理标本；(2)集中收集、处理、储存和分析样本；以及(3) 维护一个可通过整个联盟数据储存库与临床数据链接的生物检验库； (4)促进人类死后组织的收集，以加快发现创伤后应激障碍生物标志物；以及 (5)与专业知识联系，促进将生物标记物发现转化为诊断和预后小组 (例如，Lee Hood和系统生物学研究所)。生物标记物和基因组学核心将利用 在过去四年中，作为Strong Star的一部分开发了广泛的基础设施，以加速 创伤后应激障碍的生物标志物研究。此外，通过我们与NCPTSD的合作安排，我们已经 在Gelertner博士的指导下，扩展到包括耶鲁大学可用的资源和专业知识。 生物标志物和基因组学核心已经开发了广泛的标准化采血程序 用于DNA、RNA和血浆碱基蛋白质和microRNA研究的标本。标准运行 已经开发了基于PAX基因的DNA/RNA收集和自动提取的程序 为下游应用优化样品产量的数量和质量的程序。此外, 我们已经改进了用于下游蛋白质组和microRNA应用的血浆采集方法， 将促进K.Young和L.Hood博士提出的工作(见项目3)。核心区容纳了200,000人 位于UTHSCSA的最先进的研究设施--南得克萨斯研究设施的面积为2平方英尺。堆芯 分析基础架构包括具有Tecan自动化功能的Illumina iScan(微阵列)、Illumina MiSeq(小型 Scale NextGen测序)、Illumina HiSeq(大规模NextGen测序)、Fluidigm BioMark HD(REAL- 时间聚合酶链式反应)、QIAN PYROMARK Q96 MD(靶向测序/甲基化)和Luminex FlexMap 3D (多重分析物分析)。除了用于下游分析的最先进的翻译技术之外， 生物标记物和基因组学核心还包含强大的STAR-CAP生物存储库。生物储存库有 在一个安全的刷卡房间内可容纳24个冰柜(-80/-130)的容量。所有的冰柜都被实时监控- UTHSCSA网络上的时间，通过短信、电子邮件和电话发送温度通知 以及在虚拟服务器上维护的1分钟纪元冰柜日志。所有样品都被广泛地编目，使用 Freezer致力于通过相关的衍生品追踪样品的原产地。使用这些数据， 统计和知识库核心，我们目前正在开发集成生物仓库信息的系统 在Freezer中，使用存储库数据集以便于将临床和生物标记物数据与样本相关联 可用性。 在Strong STAR-CAP中，我们与UTHSCSA的西南脑库(P.Thompson&D. Cruz)添加到人类尸检组织集合中(目前总共180个大脑，10个来自 创伤后应激障碍患者)显著扩大创伤后应激障碍大脑的可获得性(通过瞄准大VA 圣安东尼奥人口)支持项目3(威廉姆森和胡德)中拟议的生物标记物发现 以及该联盟支持的未来研究。此外，生物标志物和基因组学核心将 还促进在退伍军人管理局研究中收集血液样本(约400/年)，由Acierno博士和 同事们。

Biomarkers and Genomics Core The primary objectives of the Biomarkers and Genomics Core are to (1) support the efforts of STRONG STAR- CAP studies with biomarker or genomic components involving the collection and analysis of biological and physiological specimens; (2) to centralize the collection, processing, storage, and analysis of samples; and (3) to maintain a biospecimen repository linkable with clinical data through the overall Consortium data repository; (4) facilitate the collection of human postmortem tissue in order to accelerate PTSD biomarker discovery; and (5) link with expertise to facilitate the translation of biomarker discovery into diagnostic and prognostic panels (e.g., Lee Hood and the Institute for Systems Biology). The Biomarkers and Genomics Core will make use of an extensive infrastructure developed as part of STRONG STAR over the last four years for accelerating biomarker studies of PTSD. In addition, through our partnering arrangement with the NCPTSD, we have expanded to include the resources and expertise available at Yale University as directed by Dr. Gelertner. The Biomarkers and Genomics Core has developed extensive standardized procedures for collecting blood specimens for use in DNA, RNA, and plasma base protein and microRNA research. Standard operating procedures have been developed for PAXgene-based DNA/RNA collection and automated extraction procedures to optimize the quantity and quality of the sample yields for downstream applications. In addition, we have refined the methods for plasma collection for downstream proteomic and microRNA applications that will facilitate the proposed work by Drs. K. Young and L. Hood (see Project 3). The Core is housed in 200,000 square feet of a state-of-the-art research facility, the South Texas Research Facility, located at UTHSCSA. Core analytic infrastructure includes Illumina iScan with Tecan automation (microarray), Illumina MiSeq (small- scale NextGen sequencing), Illumina HiSeq (large-scale NextGen sequencing), Fluidigm Biomark HD (real- time PCR), Qiagen Pyromark Q96 MD (targeted sequencing/methylation), and Luminex FlexMap 3D (multiplex analyte analysis). In addition to state-of-the-art translational technologies for downstream analyses, the Biomarkers and Genomics Core also houses the STRONG STAR-CAP biorepository. The biorepository has the capacity for housing 24 freezers (-80/-130) in a secure card-accessed room. All freezers are monitored real- time on the UTHSCSA network with temperature notifications delivered via text message, e-mail, and by phone and 1-minute epoch freezer logs maintained on a virtual server. All samples are extensively catalogued using Freezerworks to track samples from their origin through their associated derivatives. Working with the Data, Statistics, and Repository Core, we are currently developing systems integrating the biorepository information in Freezerworks with the repository dataset to facilitate linking clinical and biomarker data with sample availability. In STRONG STAR-CAP, we have partnered with the Southwest Brain Bank at UTHSCSA (P. Thompson & D. Cruz) to add to the collection of human postmortem tissue (currently 180 brains overall and 10 brains from persons with PTSD) to significantly expand the availability of PTSD brains (by targeting the large VA population in San Antonio) to support the proposed biomarker discovery in Project 3 (Williamson & Hood) as well as for future studies supported by the Consortium. In addition, the Biomarkers and Genomics Core will also facilitate the collection of blood specimens in VA studies (~400/year) being collected by Dr. Acierno and colleagues.