Focus on Clinical Bioinformatics: Bridging the gap between data science and medicine

“Stick out your tongue and say... ‘omics’”.
In addition to patients’ vital signs or eating habits, molecular profiling data is increasingly becoming part of the medical practitioners’ toolbox. But these ‘omics’ data pose novel challenges, for clinicians and scientists alike.

SIB’s Clinical Bioinformatics group aims at providing health professionals with expertise and support for the organization, analysis and interpretation of patient molecular data, so that they may be used for diagnosis purpose.

Since January 2017, Valérie Barbié is heading the SIB Clinical Bioinformatics group, a team composed of Aitana Lebrand (project manager), Daniel Lew (external consultant) and Yann Christinat (HUG-embedded bioinformatician).

The group is building a collaborative clinical bioinformatics community in Switzerland, around several core activities.

Swiss-wide working groups. These groups gather clinical and data science experts on specific issues. Two such groups, focusing on Next-Generation Sequencing (NGS), have already been launched, each bringing together about 50 members from a large range of institutions, including major hospitals and universities:

  • In oncology and hemato-oncology, the Somatic Mutation Calling Working Group, co-led by SIB Group Leaders N. Beerenwinkel and D. Stekhoven together with V. Barbié. An inter-laboratory test is currently in preparation with the Bioinformatics Core Facility to benchmark the bioinformatics tools used by these institutions.
  • In infectious diseases, the Microbes Typing and Characterization Working Group focuses mainly on virology and bacteriology and is co-led by SIB Group Leader R. Bruggmann together with A. Lebrand.

Partnerships with hospitals. In October 2016, the successful collaboration between SIB’s Clinical Bioinformatics and Vital-IT groups, and the University Hospitals of Geneva’s (HUG) Molecular Pathology laboratory led to the development of a streamlined bioinformatics tool for the NGS-based molecular diagnosis of cancer patients. The tool, OncoBenchTM, is used routinely since then. Read more

Training and Outreach in collaboration with SIB Outreach and Training teams. Clinical Bioinformatics was for example present at the Planète Santé public health event last November, engaging a wide audience to some of the technical and ethical challenges posed by the future of medicine. Trainings for clinicians are also developed to match their needs in the bioinformatics field.

Clinical research requests. “At SIB Clinical Bioinformatics, we also act as ‘matchmakers’ between SIB’s data science experts and clinicians”, says Aitana Lebrand.
Thanks to its tight collaboration with hospitals, the team regularly receives requests to provide bioinformatics support for clinical research projects. The group therefore continuously looks for matching expertise among SIB groups, creating new opportunities for SIB researchers to engage in clinical bioinformatics.

Watch the video ‘Bridging the gap between data science and medicine’: