{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T03:24:46Z","timestamp":1775705086312,"version":"3.50.1"},"reference-count":154,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T00:00:00Z","timestamp":1620604800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"publisher","award":["01ZZ1802"],"award-info":[{"award-number":["01ZZ1802"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001661","name":"University of Heidelberg","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001663","name":"VolkswagenStiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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.<\/jats:p>","DOI":"10.1093\/bib\/bbab134","type":"journal-article","created":{"date-parts":[[2021,4,15]],"date-time":"2021-04-15T00:07:30Z","timestamp":1618445250000},"source":"Crossref","is-referenced-by-count":21,"title":["Knowledge bases and software support for variant interpretation in precision oncology"],"prefix":"10.1093","volume":"22","author":[{"given":"Florian","family":"Borchert","sequence":"first","affiliation":[{"name":"Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany"}]},{"given":"Andreas","family":"Mock","sequence":"additional","affiliation":[{"name":"Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"},{"name":"Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"}]},{"given":"Aurelie","family":"Tomczak","sequence":"additional","affiliation":[{"name":"Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany"},{"name":"Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"}]},{"given":"Jonas","family":"H\u00fcgel","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics, University Medical Center G\u00f6ttingen, Von-Siebold-Str. 3, 37099 G\u00f6ttingen, Germany"},{"name":"Campus Institute Data Science, G\u00f6ttingen, Germany"}]},{"given":"Samer","family":"Alkarkoukly","sequence":"additional","affiliation":[{"name":"CECAD, Faculty of Medicine and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Stra\u00dfe 26, 50931 Cologne"}]},{"given":"Alexander","family":"Knurr","sequence":"additional","affiliation":[{"name":"Division of Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"}]},{"given":"Anna-Lena","family":"Volckmar","sequence":"additional","affiliation":[{"name":"Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany"}]},{"given":"Albrecht","family":"Stenzinger","sequence":"additional","affiliation":[{"name":"Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany"}]},{"given":"Peter","family":"Schirmacher","sequence":"additional","affiliation":[{"name":"Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany"},{"name":"Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"}]},{"given":"J\u00fcrgen","family":"Debus","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany"},{"name":"National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"},{"name":"Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"},{"name":"Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany"},{"name":"Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany"}]},{"given":"Dirk","family":"J\u00e4ger","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"},{"name":"Clinical Coorporation Unit Applied Tumor-Immunity, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"}]},{"given":"Thomas","family":"Longerich","sequence":"additional","affiliation":[{"name":"Institute of Pathology Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany"},{"name":"Liver Cancer Center Heidelberg, Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"}]},{"given":"Stefan","family":"Fr\u00f6hling","sequence":"additional","affiliation":[{"name":"Department of Translational Medical Oncology (TMO), National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"},{"name":"German Cancer Consortium (DKTK), 69120 Heidelberg, Germany"}]},{"given":"Roland","family":"Eils","sequence":"additional","affiliation":[{"name":"Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany"},{"name":"Center for Digital Health, Berlin Institute of Health and Charit\u00e9 Universit\u00f6tsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany"}]},{"given":"Nina","family":"Bougatf","sequence":"additional","affiliation":[{"name":"Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany"},{"name":"National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany"},{"name":"Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany"},{"name":"Heidelberg Ion-Beam Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 450, 69120 Heidelberg, Germany"},{"name":"Heidelberg Institute of Radiation Oncology (HIRO), Heidelberg University Hospital, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany"}]},{"given":"Ulrich","family":"Sax","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics, University Medical Center G\u00f6ttingen, Von-Siebold-Str. 3, 37099 G\u00f6ttingen, Germany"},{"name":"Campus Institute Data Science, G\u00f6ttingen, Germany"}]},{"given":"Matthieu-P","family":"Schapranow","sequence":"additional","affiliation":[{"name":"Digital Health Center, Hasso Plattner Institute (HPI), University of Potsdam, Prof.-Dr.-Helmert-Str. 2-3, 14482 Potsdam, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,5,10]]},"reference":[{"issue":"8","key":"2021110814295981100_ref1","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.1002\/pbc.26002","article-title":"Integrating genomics into clinical pediatric oncology using the molecular tumor board at the Memorial 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