Our bioinformatics activities broadly follow the main research topics of the Institute of Oncology Research (IOR), which is the main facility for basic and translational research at the Oncology Institute of Southern Switzerland (IOSI), the comprehensive cancer centre of the Ticino cantonal hospitals. Current research topics include the study of oncogenic transcription factors, non-coding RNA, cellular senescence, drug testing, and lymphoma pathogenesis. In collaboration with the IDSIA Dalle Molle Institute for Artificial Intelligence, we develop new algorithms for genomic and functional analysis. Our ambition for the future is to extend our bioinformatics further to the clinical and machine learning side in collaboration with the clinical groups at IOSI and the computer science groups at IDSIA. The main bioinformatics projects include:

Genomic profiling

We perform genomic profiling and bioinformatics analysis to characterize cancer types on standard microarray platforms for genome-wide gene expression profiling, methylation profiling, DNA copy number and LOH analysis. We have extensive experience in copy number profiling of lymphoid neoplasms. Recently, we also started genomic profiling of mouse specimens and perform cross species oncogenomic analysis.

Sequencing analysis

For our projects, we foresee an increase and gradual shift from microarray towards next generation sequencing. This is specifically relevant for ongoing and future projects in the area of non-coding transcripts. Developing and maintaining a sequencing analysis pipeline will become a sizeable part of the IOR bioinformatics.

Systems biology

Cancer is not caused by a single gene but through complex interactions of multiple genes. Our efforts are to go beyond single gene statistics and pursue functional analysis on gene sets and interaction networks. In a recent project we used optimization on Steiner trees to find functional correlated subnetworks that may point to driving oncogenetic pathways.

Pharmacogenomics

Pharmacogenomics is the study of the role of genomics in drug response and will be the cornerstone for personalized cancer therapy. In collaboration with pharmaceutical companies we are testing new compounds and matching drug sensitivity data with gene expression and genomic profiling data to identify novel clinically relevant biomarkers of drug response.

More information about our research