Focus on the group's purpose

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 diagnostics 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.

Clinical BioinformaticsGroup infography2019 web

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:

  • Developing and optimizing 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 4);
  • Currently developing 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, from the patient's medical visit to the lab work and results interpretation.

Supporting nationwide clinical research, surveillance, diagnostic

Thanks to its long-lasting collaboration with hospitals and other health institutions, the Group develops national collaborative solutions to support omics research, pathogen surveillance and clinical diagnostic. Recent examples include:

  • 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 (funded by SPHN and BioMedIT);
  • Collaborating with several hospitals and veterinary institutions on the development of the Swiss Pathogen Surveillance Platform (SPSP), based on whole genome sequencing of multi-drug resistant bacteria and other pathogens (funded by NRP72);
  • Currently 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 (funded by SPHN).

Fostering harmonization of clinical NGS analyses

To harmonize next-generation sequencing (NGS) practices in the clinical realm, SIB Clinical Bioinformatics is leading two working groups bringing together all university hospitals and major research institutions of Switzerland:

  • for the analysis and interpretation of genetic variants in cancer diagnosis (WG1 - Somatic Mutation Calling), and;
  • for surveillance and the diagnosis of infectious diseases, in virology and bacteriology (WG2 - Microbes Typing and Characterization).

These collaborations have led to several benchmarks of next generation sequencing (NGS) practices across hospitals in Switzerland, and to the proposal of national medical guidelines for NGS.

clinical bio map v2

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.

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 by SIB Clinical Bioinformatics in collaboration with HUG Molecular Pathology;
  • A Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology is coordinated 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;
  • A course has also been organized in clinical microbiology together with the Lausanne University Hospital and European Society for Clinical Microbiology and Infectious Diseases (ESCMID).

Publications

T. Junier et al.
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.
Genes 2019, doi: 10.3390/genes10090655

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 Weekly 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

Group Members

Valérie Barbié (Group Leader)

Ivo de Carvalho (Trainee)

Aitana Lebrand (Senior Project Manager)

Steffen Pade (Web Developer)

Florent Tassy (Clinical Data Manager)

Dillenn Terumalai (Web Developer)

Miriam Tesfai (Assistant)

Embedded bioinformaticians

Yann Christinat (University Hospitals of Geneva, HUG)

Abdullah Kahraman (University Hospital of Zürich, USZ)

Other interesting links

sib picto article web CQFD - Pathogen sequencing to monitor epidemics (FR)

sib picto article web Articles in the Bulletin of Swiss Doctors:
  • Tomorrow's health, already within the reach of doctors (FR) (DE)
  • Molecular medicine is becoming more and more important every day (FR) (DE)
sib picto article web SantéPerSo platform - Clinical bioinformaticians are key players in personalized medicine (FR