TY  - JOUR
AU  - Borchert, Florian
AU  - Mock, Andreas
AU  - Tomczak, Aurelie
AU  - Hügel, Jonas
AU  - Alkarkoukly, Samer
AU  - Knurr, Alexander
AU  - Volckmar, Anna-Lena
AU  - Stenzinger, Albrecht
AU  - Schirmacher, Peter
AU  - Debus, Jürgen
AU  - Jäger, Dirk
AU  - Longerich, Thomas
AU  - Fröhling, Stefan
AU  - Eils, Roland
AU  - Bougatf, Nina
AU  - Sax, Ulrich
AU  - Schapranow, Matthieu-P
TI  - Knowledge bases and software support for variant interpretation in precision oncology.
JO  - Briefings in bioinformatics
VL  - 22
IS  - 6
SN  - 1477-4054
CY  - Oxford [u.a.]
PB  - Oxford University Press
M1  - DKFZ-2021-01056
SP  - bbab134
PY  - 2021
N1  - 2021 Nov 5;22(6):bbab134 / 319H
AB  - 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.
KW  - HiGHmed (Other)
KW  - cancer therapy (Other)
KW  - data integration (Other)
KW  - molecular tumor board (Other)
KW  - personalized medicine (Other)
LB  - PUB:(DE-HGF)16
C6  - pmid:33971666
DO  - DOI:10.1093/bib/bbab134
UR  - https://inrepo02.dkfz.de/record/168775
ER  -