The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations.
The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations.
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DOI：
10.1093/jamia/ocw148
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发表时间：
2017-05-01
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影响因子：
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通讯作者：
Elemento O
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作者：
Huang L;Fernandes H;Zia H;Tavassoli P;Rennert H;Pisapia D;Imielinski M;Sboner A;Rubin MA;Kluk M;Elemento O
目的：本文描述了精确医学知识库(PMKB；https://pmkb.weill.cornell.edu)，)，这是一个用于协作编辑、维护和共享结构化临床级别癌症突变解释的交互式在线应用程序。材料和方法：PMKB是使用Ruby on rails Web应用程序框架构建的。利用现有的标准，如人类基因组变异协会变异描述格式，我们实现了一个数据模型，将变异与肿瘤特异性和组织特异性解释联系起来。PMKB的主要功能包括支持所有主要的变体类型、标准化的身份验证、独特的用户角色(包括高级审批人)和详细的活动历史记录。实现了一个表述性状态转移(REST)应用程序编程接口(API)来以编程方式查询PMKB。结果：在撰写本文时，PMKB包含457个不同的描述和281个临床级别的解释。EGFR、BRAF、KRAS和KIT基因与最大数量的可解释变体相关。PMKB的解释已经用于1500多个AmpliSeq测试和750个完整外显子组测序测试。这些解释可以直接通过Web接口访问，也可以通过现有API以编程方式访问。讨论：具有临床意义的基因组改变的准确和最新的知识库对于精确医学计划的成功至关重要。开放获取、可编程访问的PMKB代表了在肿瘤学领域创建这样一个资源的重要尝试。结论：PMKB旨在帮助收集和维护临床级别的突变解释，并促进临床癌症基因组检测的报告。PMKB还被设计为能够通过API创建临床癌症基因组学自动报告管道。
Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations. Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically. Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API. Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology. Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.