Focus on the group's purpose

The group's objectives are to harmonize and standardize clinical bioinformatics analysis pipelines for omics (and other high-throughput) data across hospitals in Switzerland.

Clinical BioinformaticsGroup infography2019 web

Fostering harmonization of clinical NGS analyses

The Clinical Bioinformatics group has launched working groups with university hospitals of Switzerland to harmonize next-generation sequencing (NGS) practices:

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

Thanks to its implication with the hospitals, the group is co-leading the Swiss Variant Interpretation Platform (SVIP) for oncology to provide a central resource for clinicians to establish common clinical interpretations of their patients' cancer variants. This project is part of the BioMedIT program led by SIB in the framework of the national initiative SPHN.
The group is also collaborating with several hospitals on the development of a Swiss Pathogen Surveillance Platform (SPSP), based on whole genome sequencing data of multi-drug resistant bacteria.

clinical bio map v2

Partnering with hospitals for state-of-the-art diagnostic tools

The University Hospital of Geneva and SIB are jointly developing and improving OncoBench®, a sample-to-report tool used by HUG Molecular Pathology since 2016 for the management and analysis of NGS patient data in routine cancer diagnosis (currently in version 2).
The Institute of Medical Genetics of Zürich has entered the partnership in 2017, to further collaborate on the development of a tool serving the specific needs of medical genetics.

Providing clinical bioinformatics training across Switzerland

In collaboration with HUG Molecular Pathology, the Clinical Bioinformatics group made a major step forward in the training of clinicians, with its first training course for clinical lab professionals in September 2017. This course on NGS quality control and annotation for diagnostics was successfully repeated in September 2018.

It has also partnered with the University Hospitals of Basel and Lausanne to set up a multi-disciplinary and multi-site Certificate of Advanced Studies (CAS) in Personalized Molecular Oncology. First of its kind in Switzerland, this programme coordinated by Clinical Bioinformatics aims at training the next generation of professionals from various backgrounds in this rapidly evolving field.

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 of Clinical Bioinformatics)

Aitana Lebrand (Clinical Bioinformatics Project Manager)

Florent Tassy (Clinical Data Manager and UX Designer)

Valérie Hinard (Curation expert)

Dillenn Terumalai (Web Developer)

Steffen Pade (Web Developer)

Embedded bioinformaticians

Yann Christinat (University hospitals of Geneva, HUG)

Abdullah Kahraman (USZ, Institute for Pathology and Molecular Pathology)