gms | German Medical Science

66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e. V. (TMF)

26. - 30.09.2021, online

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Introducing Variant Browser – a Meta Search Plattform for Genetic Variants

Meeting Abstract

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  • Stefan Sigle - MOLIT Institute gGmbH, Heilbronn, Germany
  • Kevin Kaufmes - MOLIT Institute gGmbH, Heilbronn, Germany
  • Patrick Werner - MOLIT Institute gGmbH, Heilbronn, Germany
  • Sylvia Bochum - SLK Clinics Heilbronn, Heilbronn, Germany
  • Uwe Martens - MOLIT Institute gGmbH, Heilbronn, Germany
  • Christian Fegeler - Heilbronn University of Applied Sciences, Heilbronn, Germany

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 66. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS), 12. Jahreskongress der Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V. (TMF). sine loco [digital], 26.-30.09.2021. Düsseldorf: German Medical Science GMS Publishing House; 2021. DocAbstr. 48

doi: 10.3205/21gmds054, urn:nbn:de:0183-21gmds0549

Veröffentlicht: 24. September 2021

© 2021 Sigle et al.
Dieser Artikel ist ein Open-Access-Artikel und steht unter den Lizenzbedingungen der Creative Commons Attribution 4.0 License (Namensnennung). Lizenz-Angaben siehe http://creativecommons.org/licenses/by/4.0/.

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Text

Introduction: Revision of annotated data generated by a broad genomic panel (>500 genes) within oncological precision medicine exceeds the resources of a single expert [1] and requires clinical decision support [2]. In order to provide personalized therapy recommendations during a multidisciplinary molecular tumor board (MTB) targeted drug therapies, clinical trials and genetic alterations have to be taken into consideration. As a consequence, the preparation time per case is drastically increased compared to traditional clinical guideline approaches [3], [4].

Methods: Available Knowledge databases (KD) [5], [6], [7], [8], [9], [10], [11], [12] were identified by literature research and evaluated for their application programming interface (API) capabilities. KDs were evaluated on the basis of their content and information retrieval capabilities. The following key factors could be identified: genetic variants, disease processes, drugs and clinical trials. Additionally, terms of service (TOS) of all KDs have been analyzed before inclusion. Variant Browser (VB) was implemented as web-application and the leveraged information sources compared to an existing meta search engine [13].

Results: VB integrates 8 of the 21 identified KDs, which comply to requirements of API accessibility as well as TOS. Only one available KD provided the possibility to define queries for genetic variants while also including additional semantical information like the reference genome sequence information, which is crucial to ensure accurate variant results. Focusing on aspects like transparency and user experience, VB can be customized to fit the user’s information need by a responsive design and dynamically adjustable table views hiding information deemed unnecessary by the user.

Discussion: API search capabilities, information models and nomenclatures of KDs impose serious limitations on knowledge integration due to i) inconsistent naming systems, ii) non-unique data standards and iii) differing taxonomy conventions for genetic variants [14]. Also, multiple queried APIs eventually change their underlying information model, while parameters like update rate and adaptation rate of new evidence into each KD remain unknown. Thus, VB pursues a platform agnostic paradigm, facilitating digital workflow integration within the context of MTB preparation.

Conclusion: Heterogeneous information models and varying semantical depth of different APIs impose limitations on knowledge integration and impact automated decision support. The aspect of enabling the standards-based integration of information found by VB into existing software frameworks and solutions for MTBs is a crucial extension to the current set of features. This prototype tackles the challenge of supporting decentralized Information gathering, but further real-world, user centered, evaluation has to be conducted within a precision medicine setting in MTB preparation to fully leverage the potential of decision support.

The MOLIT Institute is a non-profit organization, funded by donation. The last two authors are the founders of the MOLIT Institute.

The authors declare that an ethics committee vote is not required.

Gliederung

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