Focus on the group's mission
SIB Clinical Bioinformatics provides expertise and support for the organization, analysis and interpretation of patient-related data (e.g. omics data), converting them into clinically useful information for health professionals in order to foster optimal patients' care.
The group notably contributes to:
- Establishing common good practices for diagnostic omics analyses across Swiss hospitals;
- Developing national collaborative platforms to support clinical research, surveillance and diagnostic;
- Building partnerships with Swiss hospitals and industry to develop, implement and sustain state-of-the-art tools;
- Providing clinical bioinformatics training across Switzerland.
State-of-the-art diagnostic tools for hospitals
Through partnerships with hospitals, the group develops sample-to-report diagnostic tools that enable to streamline and automate bioinformatics analysis of patient data, while ensuring their privacy. Recent examples include:
- Developed the sample-to-report tool OncoBench®, with the Geneva University Hospitals (HUG). It is used by HUG Molecular Pathology since 2016 for the management and analysis of NGS patient data in routine cancer diagnosis (currently in version 5);
- Developing GenBench, a patient- and lab analysis management tool, together with the Institute of Medical Genetics of Zurich. The tool serves the specific needs of medical genetics diagnostics. It enables patient monitoring along several dimensions, from the patient's medical visit to the lab work and results interpretation.
Supporting nationwide clinical research, surveillance, diagnostic
The group develops national collaborative solutions to support omics research, pathogen surveillance and clinical diagnostic. Recent examples include:
- Co-leading with several hospitals and veterinary institutions the Swiss Pathogen Surveillance Platform (SPSP), for whole genome sequencing of multi-drug resistant bacteria and other pathogens such as SARS-CoV-2 (funded by the State Secretariat for Research and Education and the Federal Office of Public Health);
- Co-leading the Swiss Variant Interpretation Platform for Oncology (SVIP-O), a central resource for clinicians to establish common clinical interpretations of cancer variants identified in patients (initially funded by SPHN and BioMedIT);
- Developing the SwissGenVar Platform, a nation-wide effort connecting for the first time all major academic institutions for Medical Genetics in Switzerland. It integrates diagnostic-grade genetic variants interpretation and high-quality clinical data (initially funded by SPHN).
Addressing industry needs
The group partners with biotech or pharma industry on establishing new bioinformatics tools in various fields, for example imaging or genotyping, while leveraging the breadth of expertise available at SIB:
- In collaboration with Lunaphore and the Geneva University Hospitals, generated machine learning solutions to power the analysis of molecular imagery to support the characterization of tumour microenvironments;
- For a Swiss pharmaceutical company, development of a quality control signal analysis and technology assessment tool for bacterial genotyping in the context of drug production.
- Melanie is our commercial off-the-shelf software for the analysis of 2D electrophoresis gel and blot images, supporting the discovery of protein biomarkers, monitoring the adaptation of organisms to their environment, development of diagnostic tests, quality control of food samples, and development of HCP ELISA tests (choice and validation of immunoassay reagents).
Providing clinical bioinformatics training across Switzerland
Training in clinical bioinformatics for clinical professionals contributes to enhanced communication across experts from various disciplines and better use of these novel technologies in daily routine:
- A yearly training course for clinical laboratories on NGS quality control and annotation for cancer diagnosis is run since 2017 in collaboration with HUG Molecular Pathology;
- A Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology is coordinated since 2018 by the group in collaboration with the University Hospitals of Basel and Lausanne and the University of Basel. First of its kind in Switzerland, this multi-disciplinary and multi-site programme aims at training the next generation of professionals from various backgrounds in this rapidly evolving field;
Molecular medicine and the CAS in Personalized Molecular Oncology: Bulletin des médecins suisses
- Aitana Neves et al.
The Swiss Pathogen Surveillance Platform – towards a nation-wide One Health data exchange platform for bacterial, viral and fungal genomics and associated metadata.
Microbial Genomics, doi: 10.1099/mgen.0.001001
- JJC de Vries et al.
Benchmark of Thirteen Bioinformatic Pipelines for Metagenomic Virus Diagnostics Using Datasets from Clinical Samples.
Journal of Clinical Virology : The Official Publication of the Pan American Society for Clinical Virology, doi: 10.1016/j.jcv.2021.104908
- JJC de Vries et al.
Recommendations for the Introduction of Metagenomic Next-Generation Sequencing in Clinical Virology, Part II: Bioinformatic Analysis and Reporting.
Journal of Clinical Virology : The Official Publication of the Pan American Society for Clinical Virology, doi: 10.1016/j.jcv.2021.104812
- G. Greub et al.
Clinical Bioinformatics for Microbial Genomics and Metagenomics: An ESCMID Postgraduate Technical Workshop.
Microbes and Infection, doi: 10.1016/j.micinf.2020.07.008
- D. Dylus et al.
NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test.
Frontiers 2020, doi: 10.3389/fmicb.2020.591093
- A. David et al.
Annotation and curation of human genomic variations: an ELIXIR Implementation Study.
F1000Research 2020, doi: 10.12688/f1000research.24427.1
- A. Egli et al.
Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform.
Swiss Med Wkly 2018, doi: 10.4414/smw.2018.14693
- D. Wüthrich et al.
Modern Microbiological Surveillance for Antibiotic Drug Resistance.
Swiss Antibiotic Resistance Report 2018, FOPH publication number: 2018-OEG-87, 93-95
- D. Stekhoven et al.
Swiss Variant Interpretation Platform for Oncology (SVIP-O).
Swiss Med Informatics. 2018, doi: https://doi.org/10.4414/smi.34.00411
- V. Barbié et al.
La santé de demain déjà à la portée des médecins.
Bulletin des Médecins Suisses 2018, doi: https://doi.org/10.4414/bms.2018.06782
- SIB Swiss Institute of Bioinformatics members
The SIB Swiss Institute of Bioinformatics\' resources: focus on curated databases.
Nucleic Acids Res. 2016, doi: 10.1093/nar/gkv1310
- VB Gerritsen et al.
Bioinformatics and personalized medicine: Switzerland is pioneer.
Rev Med Suisse 2016; 12 : 414-6
- JS. Beckmann et al.
Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities.
Genome Medicine (2016), doi: 10.1186/s13073-016-0388-7
View our group members here