Knowledge bases and software support for variant interpretation in precision oncology Article Swipe
Florian Borchert
,
Andreas Möck
,
Aurelie Tomczak
,
Jonas Hügel
,
Samer Alkarkoukly
,
Alexander Knurr
,
Anna‐Lena Volckmar
,
Albrecht Stenzinger
,
Peter Schirmacher
,
Jürgen Debus
,
Dirk Jäger
,
Thomas Longerich
,
Stefan Fröhling
,
Roland Eils
,
Nina Bougatf
,
Ulrich Sax
,
Matthieu-P. Schapranow
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbab134
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbab134
Precision oncology is a rapidly evolving interdisciplinary medical specialty. Comprehensive cancer panels are becoming increasingly available at pathology departments worldwide, creating the urgent need for scalable cancer variant annotation and molecularly informed treatment recommendations. A wealth of mainly academia-driven knowledge bases calls for software tools supporting the multi-step diagnostic process. We derive a comprehensive list of knowledge bases relevant for variant interpretation by a review of existing literature followed by a survey among medical experts from university hospitals in Germany. In addition, we review cancer variant interpretation tools, which integrate multiple knowledge bases. We categorize the knowledge bases along the diagnostic process in precision oncology and analyze programmatic access options as well as the integration of knowledge bases into software tools. The most commonly used knowledge bases provide good programmatic access options and have been integrated into a range of software tools. For the wider set of knowledge bases, access options vary across different parts of the diagnostic process. Programmatic access is limited for information regarding clinical classifications of variants and for therapy recommendations. The main issue for databases used for biological classification of pathogenic variants and pathway context information is the lack of standardized interfaces. There is no single cancer variant interpretation tool that integrates all identified knowledge bases. Specialized tools are available and need to be further developed for different steps in the diagnostic process.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bib/bbab134
- https://academic.oup.com/bib/article-pdf/22/6/bbab134/41087588/bbab134.pdf
- OA Status
- hybrid
- Cited By
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- References
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- Related Works
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- OpenAlex ID
- https://openalex.org/W3161121057
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3161121057Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bib/bbab134Digital Object Identifier
- Title
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Knowledge bases and software support for variant interpretation in precision oncologyWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2021Year of publication
- Publication date
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2021-04-15Full publication date if available
- Authors
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Florian Borchert, Andreas Möck, Aurelie Tomczak, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna‐Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P. SchapranowList of authors in order
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https://doi.org/10.1093/bib/bbab134Publisher landing page
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https://academic.oup.com/bib/article-pdf/22/6/bbab134/41087588/bbab134.pdfDirect link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://academic.oup.com/bib/article-pdf/22/6/bbab134/41087588/bbab134.pdfDirect OA link when available
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Computer science, Context (archaeology), Process (computing), Categorization, Annotation, Data science, Interpretation (philosophy), Set (abstract data type), Software, Knowledge management, Artificial intelligence, Operating system, Programming language, Biology, PaleontologyTop concepts (fields/topics) attached by OpenAlex
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22Total citation count in OpenAlex
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2025: 6, 2024: 5, 2023: 4, 2022: 4, 2021: 3Per-year citation counts (last 5 years)
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175Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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