ArticleJCO precision oncology2019
Comparative Analysis of Public Knowledge Bases for Precision Oncology.
Article in JCO precision oncology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 67 citations in OpenAlex.
- Concordance in Molecular Tumor Board Case Reviews in the ASCO TAPUR Study.JCO precision oncology · 2024Trial
- Real-world performance analysis of a universal computational reasoning model for precision oncology in lung cancer.NPJ precision oncology · 2025Article
- Evidence blocks for effective presentation of genomic findings at molecular tumor boards: Single institution experience.Heliyon · 2024Article
- preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.Bioinformatics (Oxford, England) · 2024Article
- The consequences of data dispersion in genomics: a comparative analysis of data sources for precision medicine.BMC medical informatics and decision making · 2023Article
- Leveraging Large Language Models for Decision Support in Personalized Oncology.JAMA network open · 2023Article
- Utility of public knowledge bases for the interpretation of comprehensive tumor molecular profiling results.Clinical and experimental medicine · 2023Article
- Immune checkpoint inhibitor-related molecular markers predict prognosis in extrahepatic cholangiocarcinoma.Cancer medicine · 2023Article
- AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine.Database : the journal of biological databases and curation · 2023Article
- CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.Nucleic acids research · 2023Article
- Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.BMC medicine · 2022Article
- CRAC (Clinical Relevance of Alterations in Cancer): a Knowledge Base for the Selection of Molecularly Matched Therapy for Solid Tumors.Sovremennye tekhnologii v meditsine · 2022Article
- Knowledge bases and software support for variant interpretation in precision oncology.Briefings in bioinformatics · 2021Article
- [Variant interpretation in molecular pathology and oncology : An introduction].Der Pathologe · 2021Review
- Review
- [RAS mutations at the molecular tumor conference].Der Pathologe · 2019Review
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposePrecision oncology depends on the availability of up-to-date, comprehensive, and accurate information about associations between genetic variants and therapeutic options. Recently, a number of knowledge bases (KBs) have been developed that gather such information on the basis of expert curation of the scientific literature. We performed a quantitative and qualitative comparison of Clinical Interpretations of Variants in Cancer, OncoKB, Cancer Gene Census, Database of Curated Mutations, CGI Biomarkers (the cancer genome interpreter biomarker database), Tumor Alterations Relevant for Genomics-Driven Therapy, and the Precision Medicine Knowledge Base.
methodsWe downloaded each KB and restructured their content to describe variants, genes, drugs, and gene-drug associations in a common format. We normalized gene names to Entrez Gene IDs and drug names to ChEMBL and DrugBank IDs. For the analysis of clinically relevant gene-drug associations, we obtained lists of genes affected by genetic alterations and putative drug therapies for 113 patients with cancer whose cases were presented at the Molecular Tumor Board (MTB) of the Charité Comprehensive Cancer Center.
resultsOur analysis revealed that the KBs are largely overlapping but also that each source harbors a notable amount of unique information. Although some KBs cover more genes, others contain more data about gene-drug associations. Retrospective comparisons with findings of the Charitè MTB at the gene level showed that use of multiple KBs may considerably improve retrieval results. The relative importance of a KB in terms of cancer genes was assessed in more detail by logistic regression, which revealed that all but one source had a notable impact on result quality. We confirmed these findings using a second data set obtained from an independent MTB.
conclusionTo date, none of the existing publicly available KBs on gene-drug associations in precision oncology fully subsumes the others, but all of them exhibit specific strengths and weaknesses. Consideration of multiple KBs, therefore, is essential to obtain comprehensive results.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.