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SwissGenVar: A platform for clinical grade interpretation of genetic variants to foster personalized health care in Switzerland


Kraemer, Dennis; Terumalai, Dillenn; Famiglietti, Maria Livia; Filges, Isabel; Joset, Pascal; Koller, Samuel; Maurer, Fabienne; Meier, Stéphanie; Nouspikel, Thierry; Sanz, Javier; Zweier, Christiane; Abramowicz, Marc; Berger, Wolfgang; Cichon, Sven; Schaller, André; Superti-Furga, Andrea; Barbié, Valérie; Rauch, Anita (2023). SwissGenVar: A platform for clinical grade interpretation of genetic variants to foster personalized health care in Switzerland. medRxiv 22283790, Cold Spring Harbor Laboratory.

Abstract

Large-scale next-generation sequencing (NGS) germline testing is technically feasible today, but variant interpretation represents a major bottleneck in analysis workflows including the extensive variant prioritization, annotation, and time-consuming evidence curation. The scale of the interpretation problem is massive, and variants of uncertain significance (VUS) are a challenge to personalized medicine. This challenge is further compounded by the complexity and heterogeneity of standards used to describe genetic variants and associated phenotypes when searching for relevant information to inform clinical decision-making. For this purpose, all five Swiss academic Medical Genetics Institutions joined forces with the Swiss Institute of Bioinformatics (SIB) to create SwissGenVar as a user-friendly nationwide repository and sharing platform for genetic variant data generated during routine diagnostic procedures and research sequencing projects. Its objective is to provide a protected environment for expert evidence sharing about individual variants to harmonize and up-scale their significance interpretation at clinical grade following international standards. To corroborate the clinical assessment, the variant-related data are combined with consented high-quality clinical information. Broader visibility will be gained by interfacing with international databases, thus supporting global initiatives in personalized health care.

Abstract

Large-scale next-generation sequencing (NGS) germline testing is technically feasible today, but variant interpretation represents a major bottleneck in analysis workflows including the extensive variant prioritization, annotation, and time-consuming evidence curation. The scale of the interpretation problem is massive, and variants of uncertain significance (VUS) are a challenge to personalized medicine. This challenge is further compounded by the complexity and heterogeneity of standards used to describe genetic variants and associated phenotypes when searching for relevant information to inform clinical decision-making. For this purpose, all five Swiss academic Medical Genetics Institutions joined forces with the Swiss Institute of Bioinformatics (SIB) to create SwissGenVar as a user-friendly nationwide repository and sharing platform for genetic variant data generated during routine diagnostic procedures and research sequencing projects. Its objective is to provide a protected environment for expert evidence sharing about individual variants to harmonize and up-scale their significance interpretation at clinical grade following international standards. To corroborate the clinical assessment, the variant-related data are combined with consented high-quality clinical information. Broader visibility will be gained by interfacing with international databases, thus supporting global initiatives in personalized health care.

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Additional indexing

Item Type:Working Paper
Communities & Collections:04 Faculty of Medicine > Institute of Medical Genetics
04 Faculty of Medicine > Institute of Medical Molecular Genetics
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Uncontrolled Keywords:SwissGenVar, Switzerland, NGS, expert-curated variant interpretation, national mutation database, genotype-phenotype database, personalized medicine
Language:English
Date:11 January 2023
Deposited On:12 Jan 2023 09:17
Last Modified:10 Apr 2024 09:46
Series Name:medRxiv
Additional Information:Data Availability Statement: The SwissGenVar documentation and public website are available at: https://pages.sib.swiss/project/swissgenvar-doc/ and https://pages.sib.swiss/project/swissgenvar/, respectively. The project GitLab site is available at https://gitlab.sib.swiss/clinbio/swissgenvar/sgv-knowledge/-/tree/master .
OA Status:Green
Publisher DOI:https://doi.org/10.1101/2023.01.11.22283790
Project Information:
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)