TY  - JOUR
A1  - Borchert, Florian
A1  - Mock, Andreas
A1  - Tomczak, Aurelie
A1  - Hügel, Jonas
A1  - Alkarkoukly, Samer
A1  - Knurr, Alexander
A1  - Volckmar, Anna-Lena
A1  - Stenzinger, Albrecht
A1  - Schirmacher, Peter
A1  - Debus, Jürgen
A1  - Jäger, Dirk
A1  - Longerich, Thomas
A1  - Fröhling, Stefan
A1  - Eils, Roland
A1  - Bougatf, Nina
A1  - Sax, Ulrich
A1  - Schapranow, Matthieu-Patrick
T1  - Knowledge bases and software support for variant interpretation in precision oncology
JF  - Briefings in bioinformatics
N2  - 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
KW  - personalized medicine
KW  - molecular tumor board
KW  - data integration
KW  - cancer therapy
Y1  - 2021
U6  - https://doi.org/10.1093/bib/bbab134
SN  - 1467-5463
SN  - 1477-4054
VL  - 22
IS  - 6
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Borchert, Florian
A1  - Mock, Andreas
A1  - Tomczak, Aurelie
A1  - Hügel, Jonas
A1  - Alkarkoukly, Samer
A1  - Knurr, Alexander
A1  - Volckmar, Anna-Lena
A1  - Stenzinger, Albrecht
A1  - Schirmacher, Peter
A1  - Debus, Jürgen
A1  - Jäger, Dirk
A1  - Longerich, Thomas
A1  - Fröhling, Stefan
A1  - Eils, Roland
A1  - Bougatf, Nina
A1  - Sax, Ulrich
A1  - Schapranow, Matthieu-Patrick
T1  - Correction to: Knowledge bases and software support for variant interpretation in precision oncology
JF  - Briefings in bioinformatics
Y1  - 2021
U6  - https://doi.org/10.1093/bib/bbab246
SN  - 1467-5463
SN  - 1477-4054
VL  - 22
IS  - 6
PB  - Oxford Univ. Press
CY  - Oxford
ER  -