Universität zu Köln

Borchert, Florian, Mock, Andreas, Tomczak, Aurelie, Huegel, Jonas, Alkarkoukly, Samer ORCID: 0000-0003-1891-1366, Knurr, Alexander, Volckmar, Anna-Lena ORCID: 0000-0002-1036-5391, Stenzinger, Albrecht, Schirmacher, Peter, Debus, Juergen, Jaeger, Dirk, Longerich, Thomas, Froehling, Stefan, Eils, Roland ORCID: 0000-0002-0034-4036, Bougatf, Nina, Sax, Ulrich and Schapranow, Matthieu-P (2021). Knowledge bases and software support for variant interpretation in precision oncology. Brief. Bioinform., 22 (6). OXFORD: OXFORD UNIV PRESS. ISSN 1477-4054

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Borchert, Florian UNSPECIFIED UNSPECIFIED UNSPECIFIED Mock, Andreas UNSPECIFIED UNSPECIFIED UNSPECIFIED Tomczak, Aurelie UNSPECIFIED UNSPECIFIED UNSPECIFIED Huegel, Jonas UNSPECIFIED UNSPECIFIED UNSPECIFIED Alkarkoukly, Samer UNSPECIFIED orcid.org/0000-0003-1891-1366 UNSPECIFIED Knurr, Alexander UNSPECIFIED UNSPECIFIED UNSPECIFIED Volckmar, Anna-Lena UNSPECIFIED orcid.org/0000-0002-1036-5391 UNSPECIFIED Stenzinger, Albrecht UNSPECIFIED UNSPECIFIED UNSPECIFIED Schirmacher, Peter UNSPECIFIED UNSPECIFIED UNSPECIFIED Debus, Juergen UNSPECIFIED UNSPECIFIED UNSPECIFIED Jaeger, Dirk UNSPECIFIED UNSPECIFIED UNSPECIFIED Longerich, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Froehling, Stefan UNSPECIFIED UNSPECIFIED UNSPECIFIED Eils, Roland UNSPECIFIED orcid.org/0000-0002-0034-4036 UNSPECIFIED Bougatf, Nina UNSPECIFIED UNSPECIFIED UNSPECIFIED Sax, Ulrich UNSPECIFIED UNSPECIFIED UNSPECIFIED Schapranow, Matthieu-P UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-600091
DOI:	10.1093/bib/bbab134
Journal or Publication Title:	Brief. Bioinform.
Volume:	22
Number:	6
Date:	2021
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1477-4054
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language MOLECULAR TUMOR BOARD; CLINICAL INTERPRETATION; AMERICAN-SOCIETY; GENE-EXPRESSION; OPEN PLATFORM; CANCER; DATABASE; INFORMATION; GENOMICS; MUTATIONS Multiple languages Biochemical Research Methods; Mathematical & Computational Biology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/60009