What do we do?
In the Bioinformatics Core Facility (BCF) we promote trans-disciplinary collaborations between research teams in medicine, molecular biology, genetics, genomics, statistics and bioinformatics. In particular, we perform analysis of biomedical-genomics data with a focus on biomarker studies in cancer research, building on our specific expertise in statistical methods for genomics data analysis. Recently, we concentrated on molecular heterogeneity and pathway activation patterns in cancer subtypes, but we are open to any kind of research directions.
In 2015, our team investigated the molecular heterogeneity of colon cancer (CC) with the aim of finding information that is useful to assess the expected risk of metastasis and the best way to treat the disease after surgical removal. Useful information consists in predicting the benefit of chemotherapy, if it outweighs its side effects, and in predicting which drug would be more effective.
A first approach consists in a direct statistical analysis of the relationships between one tumour feature and a variable of clinical interest (such as the risk of metastasis for example). In a second approach, the group begins by subdividing the tumours into several groups which differ more clearly from one another by the characteristics of their gene expression patterns (so called tumour subtypes). We then test the usefulness of these groups with respect to the clinical interest. In this way, our team completed a collaborative investigation (Guinney et al. 2015) designed to consolidate previously proposed gene expression subtype systems including their own (Budinska et al. 2013). This investigation classifies primary CC into four major “consensus molecular subtypes” (CMS 1-4). The CMS system will be useful to assess which treatments have high efficacy in which patient groups; to this end, our lab is working with teams that have relevant clinical trial data.
Main publications 2015
- Fischer U et al. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukaemia identifies recurrent mutation patterns and therapeutic options. Nat Genet 2015;47(9):1020-9.
- Guinney J et al. The consensus molecular subtypes of colorectal cancer. Nat Med 2015;21(11):1350-6.
- Klingbiel D et al. Prognosis of stage II and III colon carcinoma treated with adjuvant 5-FU or FOLFIRI in relation to microsatellite status, results of the PETACC-3 trial. Ann Oncol 2015;26(1):126-32.