Jang Yeongjun, Choi Taekjin, Kim Jongho, Park Jisub, Seo Jihae, Kim Sangok, Kwon Yeajee, Lee Seungjae, Lee Sanghyuk
Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, Korea.
Interdisciplinary Program in Bioinformatics, College of Natural Science, Seoul National University, Seoul, Korea.
BMC Med Genomics. 2018 Apr 20;11(Suppl 2):34. doi: 10.1186/s12920-018-0347-9.
Increasing affordability of next-generation sequencing (NGS) has created an opportunity for realizing genomically-informed personalized cancer therapy as a path to precision oncology. However, the complex nature of genomic information presents a huge challenge for clinicians in interpreting the patient's genomic alterations and selecting the optimum approved or investigational therapy. An elaborate and practical information system is urgently needed to support clinical decision as well as to test clinical hypotheses quickly.
Here, we present an integrated clinical and genomic information system (CGIS) based on NGS data analyses. Major components include modules for handling clinical data, NGS data processing, variant annotation and prioritization, drug-target-pathway analysis, and population cohort explorer. We built a comprehensive knowledgebase of genes, variants, drugs by collecting annotated information from public and in-house resources. Structured reports for molecular pathology are generated using standardized terminology in order to help clinicians interpret genomic variants and utilize them for targeted cancer therapy. We also implemented many features useful for testing hypotheses to develop prognostic markers from mutation and gene expression data.
Our CGIS software is an attempt to provide useful information for both clinicians and scientists who want to explore genomic information for precision oncology.
下一代测序（NGS）成本的不断降低为实现基于基因组信息的个性化癌症治疗创造了机会，这是精准肿瘤学的一条途径。然而，基因组信息的复杂性给临床医生解读患者的基因组改变并选择最佳的获批或研究性治疗带来了巨大挑战。迫切需要一个精心设计且实用的信息系统来支持临床决策，并快速验证临床假设。
在此，我们展示了一个基于NGS数据分析的临床与基因组综合信息系统（CGIS）。主要组件包括处理临床数据、NGS数据处理、变异注释与优先级排序、药物 - 靶点 - 通路分析以及人群队列浏览器的模块。我们通过从公共和内部资源收集注释信息，构建了一个关于基因、变异、药物的综合知识库。使用标准化术语生成分子病理学的结构化报告，以帮助临床医生解读基因组变异并将其用于靶向癌症治疗。我们还实现了许多有助于从突变和基因表达数据中验证假设以开发预后标志物的功能。
我们的CGIS软件旨在为希望探索基因组信息用于精准肿瘤学的临床医生和科学家提供有用信息。
