The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research
The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research
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DOI：
10.1186/s12864-016-2797-9
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发表时间：
2016-08-18
期刊：
影响因子：
4.4
通讯作者：
Pennington, Jeffrey W.
中科院分区：
文献类型：
--
作者：
Felmeister, Alex S.;Masino, Aaron J.;Pennington, Jeffrey W.
背景资料：高通量分子测序和增加的生物标本种类为研究生物库基础设施带来了重大的信息学挑战。我们采用模块化的系统集成方法来开发一个可操作的生物库管理系统。这种方法使聚集的临床，标本和基因组数据收集biorepository resources.Methods：我们介绍了一个电子诚实的经纪人（eHB）和生物库门户网站（BRP）的开源项目，在串联，允许数据集成，同时保护患者的隐私。这种模块化的方法允许数据和标本在任何时间点异步地与生物库主题相关联。这降低了基于科学价值开发新研究项目的门槛，而无需对提案进行机构审查。结果：通过促进标本和相关临床和基因组数据的自动去识别化，我们创建了一个未来证明的标本集，可以承受新的工作流程，并随着时间的推移连接到新的相关信息。结论：截至2016年1月，在生物储存库门户（BRP）中管理着23个独特的方案/患者队列。电子诚实经纪人（eHB）中有超过4000个独特的受试者记录，超过30，000个标本被加入，8个机构使用该工具包参与各种生物库活动。我们特别着手构建具有纵向临床数据的生物标本的丰富注释;多机构存储库的BRP/REDCap集成; EMR集成;特定于某个领域的基因组数据的进一步注释标本;构建与分析软件集成的标本级实验的应用程序挂钩;同时根据民权办公室（OCR）和HIPAA保护隐私。
Background: High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of the clinical, specimen and genomic data collected for biorepository resources.Methods: We introduce an electronic Honest Broker (eHB) and Biorepository Portal (BRP) open source project that, in tandem, allow for data integration while protecting patient privacy. This modular approach allows data and specimens to be associated with a biorepository subject at any time point asynchronously. This lowers the bar to develop new research projects based on scientific merit without institutional review for a proposal.Results: By facilitating the automated de-identification of specimen and associated clinical and genomic data we create a future proofed specimen set that can withstand new workflows and be connected to new associated information over time. Thus facilitating collaborative advanced genomic and tissue research.Conclusions: As of Janurary of 2016 there are 23 unique protocols/patient cohorts being managed in the Biorepository Portal (BRP). There are over 4000 unique subject records in the electronic honest broker (eHB), over 30,000 specimens accessioned and 8 institutions participating in various biobanking activities using this tool kit. We specifically set out to build rich annotation of biospecimens with longitudinal clinical data; BRP/REDCap integration for multi-institutional repositories; EMR integration; further annotated specimens with genomic data specific to a domain; build application hooks for experiments at the specimen level integrated with analytic software; while protecting privacy per the Office of Civil Rights (OCR) and HIPAA.