肿瘤精准医学知识数据库的设计与构建

doi:10.13523/j.cb.20180506

中国生物工程杂志

2018, Vol. 38

Issue (5): 40-46 DOI: 10.13523/j.cb.20180506

研究报告

肿瘤精准医学知识数据库的设计与构建

汪凌¹,陈新^2,^*

1 浙江大学化学工程与生物工程学院杭州 310027
2 浙江大学药物生物技术研究所杭州 310058

Design and Construction of Tumor Precision Medicine Knowledge Database

Ling WANG¹,Xin CHEN^2,^*

1 College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
2 Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou 310058, China

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摘要：

目的:整合现有前沿的大量而分散的精准医学知识以形成系统完整的知识数据库,为个体组学数据的临床应用提供依据,旨在最终实现基于组学特征的精准用药推荐。方法:采用MySQL数据库管理系统构建数据库,从FDA伴随诊断、NCCN指南、My Cancer Genome、GDSC四大权威医学资源中手动收集精准用药知识,并将原始数据标准化、结构化后以统一的格式存储。结果:成功设计并构建了肿瘤精准医学知识库,目前共收录1 940条精准用药指导,涵盖了基因突变等14种不同类型的组学特征。结论:精准医学知识数据库收录了肿瘤分子组学特征和治疗策略的关联信息,可为临床上个体化治疗方案的制订提供参考依据。数据库的建立为精准医疗临床决策支持系统的开发奠定了基础。

关键词： 肿瘤; 精准医学; 数据库; 组学数据

Abstract:

Objective:To integrate substantial but scattered state-of-the-art precision medicine knowledge and form a systematic knowledge network, to support clinical application of individual omics data, aiming at precision medication recommendations.Methods:The database was constructed using MySQL. Precision medicine knowledge from FDA companion diagnosis, NCCN guidelines, My Cancer Genome and GDSC was manually collected in a unified format after being standardized and structured.Results:The tumor precision medicine knowledge base (PMKB) was successfully designed and constructed and has already collected 1 940 clinical directives, covering 14 kinds of variations.Conclusion:PMKB collects information relating tumor mutations and therapeutic strategies, which can provide personalized treatments of reference. PMKB is also the base of constructing a clinical decision support system of precision medicine.

Key words: Tumor Precision medicine Database Omics data

收稿日期: 2017-10-12 出版日期: 2018-06-05

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通讯作者: 陈新

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引用本文:

汪凌,陈新. 肿瘤精准医学知识数据库的设计与构建[J]. 中国生物工程杂志, 2018, 38(5): 40-46.

Ling WANG,Xin CHEN. Design and Construction of Tumor Precision Medicine Knowledge Database. China Biotechnology, 2018, 38(5): 40-46.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20180506 或 https://manu60.magtech.com.cn/biotech/CN/Y2018/V38/I5/40

图1 精准医学知识数据库实体关系图

表1 临床用药指导表

图2 用药指征逻辑拆分示意图

表2 综合指征表

表3 综合指征成分表

表4 分子指征表

表5 治疗策略表

表6 治疗策略成分表

表7 PMKB临床用药指导条目统计

表8 精准医学知识数据库条目统计

图3 精准医学知识搜索系统示意图

[1]	Stratton M R, Campbell P J, Futreal P A . The cancer genome. Nature, 2009,458(7239):719-724. doi: 10.1038/nature07943
[2]	付文华, 钱海利, 詹启敏 . 中国精准医学发展的需求和任务. 中国生化药物杂志, 2016,36(4):1-4.
	Fu W H, Qian H L, Zhan Q M . Precision medicine in China. Chinese Journal of Biochemical Pharmaceutics, 2016,36(4):1-4.
[3]	Garraway L A, Verweij J, Ballman K V . Precision oncology: an overview. Journal of Clinical Oncology, 2013,31(15):1803-1805. doi: 10.1200/JCO.2013.49.4799
[4]	Sorich M J, Wiese M D, Rowland A , et al. Extended RAS mutations and anti-EGFR monoclonal antibody survival benefit in metastatic colorectal cancer: a meta-analysis of randomized, controlled trials. Annals of Oncology, 2015,26(1):13-21. doi: 10.1093/annonc/mdu378 pmid: 25115304
[5]	Allegra C J, Rumble R B, Richard L S , et al. Extended RAS gene mutation testing in metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy: American society of clinical oncology provisional clinical opinion update 2015 summary. Journal of Clinical Oncology, 2016,34(2):179-185.
[6]	Ali S M, Hensing T, Schrock A B , et al. Comprehensive genomic profiling identifies a subset of crizotinib-responsive ALK-rearranged non-small cell lung cancer not detected by fluorescence in situ hybridization. Oncologist, 2016,21(6):762-770. doi: 10.1634/theoncologist.2015-0497
[7]	Rankin A, Klempner S J, Erlich R , et al. Broad detection of alterations predicted to confer Lack of benefit from EGFR antibodies or sensitivity to targeted therapy in advanced colorectal cancer. Oncologist, 2016,21(11):1306-1314. doi: 10.1634/theoncologist.2016-0148 pmid: 27682134
[8]	Boussemart, Wang A , Wong M K K, et al. Hybrid-capture based genomic profiling identifies BRAF V600 and non-V600 alterations in melanoma samples negative by prior testing. Annals of Oncology, 2017,28(suppl_5):v428-v448. doi: 10.1093/annonc/mdx377.020
[9]	Kusnoor S V, Koonce T Y, Levy M A , et al. My cancer genome: evaluating an educational model to introduce patients and caregivers to precision medicine information. AMIA Joint Summits on Translational Science, 2016,( 2016):112-121. pmid: 5001739
[10]	Levy M, Lovly C, Horn L , et al. My cancer genome: Web-based clinical decision support for genome-directed lung cancer treatment. Journal of Clinical Oncology, 2011,29(15 suppl):7576. doi: 10.1093/annonc/mdr431
[11]	Iorio F, Knijnenburg T, Vis D , et al. A landscape of pharmacogenomic interactions in cancer. Cell, 2016,166(3):740. doi: 10.1016/j.cell.2016.06.017 pmid: 27397505
[12]	Castaneda C, Nalley K, Mannion C , et al. Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine. Journal of Clinical Bioinformatics, 2015,5(1):4. doi: 10.1186/s13336-015-0019-3 pmid: 4381462
[13]	Fridlyand J, Simon R M, Walrath J C , et al. Considerations for the successful co-development of targeted cancer therapies and companion diagnostics. Nature Reviews Drug Discovery, 2013,12(10):743. doi: 10.1038/nrd4101 pmid: 24008432
[14]	Mansfield E A . FDA perspective on companion diagnostics: an evolving paradigm. Clinical Cancer Research, 2014,20(6):1453-1457. doi: 10.1158/1078-0432.CCR-13-1954 pmid: 24634468
[15]	National Comprehensive Cancer Network. About NCCN.[2017-12-27]. .
[16]	National Comprehensive Cancer Network. NCCN clinical practice guidelines in oncology: non-small cell lung.[2017-12-27]. .
[17]	Vanderbilt-Ingram Cancer Center, My Cancer Genome (Website Index). [2017-12-27]..
[18]	Yang W, Soares J, Greninger P , et al. Genomics of drug sensitivity in cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Research, 2013,41:D955-D961.
[19]	Al-Haddad M A, Friedlin J, Kesterson J , et al. Natural language processing for the development of a clinical registry: a validation study in intraductal papillary mucinous neoplasms. HPB, 2010,12(10):688-695. doi: 10.1111/j.1477-2574.2010.00235.x
[20]	Koh H C, Tan G . Data mining applications in healthcare. Journal of Healthcare Information Management, 2005,19(2):64-72. doi: 10.4314/ijonas.v5i1.49926 pmid: 15869215

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