Journal Article

DKFZ-2021-01056

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Knowledge bases and software support for variant interpretation in precision oncology.

Borchert, F. ; Mock, A.Extern* ; Tomczak, A. ; Hügel, J. ; Alkarkoukly, S.DKFZ* ; Knurr, A.DKFZ* ; Volckmar, A.-L. ; Stenzinger, A. ; Schirmacher, P.DKFZ* ; Debus, J.DKFZ* ; Jäger, D.DKFZ* ; Longerich, T. ; Fröhling, S.DKFZ* ; Eils, R. ; Bougatf, N.Extern* ; Sax, U.DKFZ* ; Schapranow, M.-P.

2021
Oxford University Press Oxford [u.a.]

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Please use a persistent id in citations: doi:10.1093/bib/bbab134

Abstract: 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.

Keyword(s): HiGHmed ; cancer therapy ; data integration ; molecular tumor board ; personalized medicine

Note: 2021 Nov 5;22(6):bbab134 / 319H

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Contributing Institute(s):

1. Clinical Trial Office (M130)
2. E050 KKE Strahlentherapie (E050)
3. Angewandte Tumor-Immunität (D120)
4. DKTK HD zentral (HD01)
5. Translationale Medizinische Onkologie (B340)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2021

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 5 ; JCR ; Nationallizenz ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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