An informatics model for tissue banks - Lessons learned from the Cooperative Prostate Cancer Tissue Resource
An informatics model for tissue banks - Lessons learned from the Cooperative Prostate Cancer Tissue Resource
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DOI：
10.1186/1471-2407-6-120
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发表时间：
2006-05-05
期刊：
影响因子：
3.8
通讯作者：
Becich, Michael J.
中科院分区：
文献类型：
--
作者：
Patel, Ashokkumar A.;Gilbertson, John R.;Becich, Michael J.
背景：分子生物学的进步和生物标记物验证研究的日益增长的要求促使组织库提供具有标准化临床注释的质量控制的组织样本。NCI合作前列腺癌组织资源(CPCTR)是一个分布式组织库，由四个学术中心组成，向研究人员提供数千个带有临床注释的前列腺癌标本。这里我们描述了CPCTR信息管理系统的体系结构、公共数据元素(CDE)的开发、查询接口、数据管理和质量控制。方法：数据管理员审查病历，收集并持续更新资源为每个病例维护的145个临床、病理和库存CDE的信息。以准入为基础的数据录入工具在每一组与CPCTR中央数据库之间提供去身份识别和标准通信机制。实施了标准化的自动化质量控制审计。在中央，Oracle数据库具有网络接口，允许包括普通公众在内的多个用户类型以三个级别的特异性和粒度从所有站点挖掘未识别的信息，并通过正式意向书请求组织。结果：自2003年7月以来，CPCTR提供了超过6,000例(38,000块)高度特征化的前列腺癌生物标本，包括几个组织微阵列(TMA)。该资源开发了一个网站，为普通公众以及研究人员和内部成员提供界面。这些用户组利用网络工具公开查询现有案件的摘要数据、准备请求和接收纸巾。截至2005年12月，资源收到130多份组织申请，其中45项已得到审查、核准和填补。此外，该资源在其TMA计划中实施了TMA数据交换规范，并创建了用于计算PSA复发率的计算机程序。结论：构建满足当今研究需求的生物信息库基础设施需要来自不同学科的许多人的时间和投入。CPCTR可以为专门的研究计划(孢子)和生物标记物验证研究等研究计划提供大量经过仔细注释的前列腺组织，其经验可以帮助在其他器官系统中开发协作的、大规模的虚拟组织库。
Background: Advances in molecular biology and growing requirements from biomarker validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control.Methods: Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent.Results: Since July 2003, CPCTR has offered over 6,000 cases ( 38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence.Conclusion: Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for biomarker validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems.