The Center of Excellence consists of four groups with complementary expertise:
- the Tumor Genomics group at the University of Helsinki, led by Lauri Aaltonen, with an excellent track record in tumor genomics and sequence analysis;
- the Medical Systems Biology group at University of Helsinki & University of Cambridge, led by Jussi Taipale, providing world-leading strength in functional genome annotation, modelling, and high-throughput screening; and
- the Computational Biology group at the University of Tampere, led by Matti Nykter, with comprehensive knowledge of bioinformatics including use of the existing omics resources; and
- the Cancer Epidemiology group at the Finnish Cancer Registry, led by Janne Pitkäniemi, representing expertise in epidemiology.
Lauri Aaltonen is the director of the CoE and his Tumor Genomics group serves as a link connecting clinical and epidemiological areas to the computational and experimental activities within the CoE. To this end the group provides expertise in clinical medicine and close collaboration with clinicians nationally as well as internationally, selection of key patient groups for analysis, solid experience in patient sample analyses and data processing, and particular expertise in the complex world of medical genetics including appropriate authorizations for use of registries and sample resources, and appropriate handling of results including incidental findings.
Jussi Taipale is the vice-director of the CoE. His Medical Systems Biology group is comprised of both experimental and computational scientists, and is responsible for evaluating the effect of the identified mutations on cancer growth and predisposition. To unravel the functions of non-coding variants, the group will improve the functional annotation of the human genome, by determining transcription factor (TF) binding specificities and TF occupied positions in the genome, and by generating other epigenomic datasets that allow localization of gene regulatory elements and their activity. This will enable improved annotation of normal and tumor genomes, and prediction of the effect of the variants and mutations identified in the genomic studies. In addition, the group provides to the CoE expertise in high-throughput screening and handling of big datasets.
Matti Nykter leads the Computational Biology group, which focuses on developing algorithms and computational models for biomedical applications. The group favors a data-driven approach which often begins with the acquisition of high throughput genomic, epigenomic, transcriptomic and/or proteomic data. The group then analyses the data computationally in an effort to better understand the biological processes and networks driving a disease or phenotype. The generated hypotheses are then validated and refined in collaboration with experimentally inclined research groups. Core competence of the group is in the methods of statistical modelling, machine learning and computer science. The group’s focus is to uncover the molecular basis of human cancers to generate new avenues for treatment and diagnostics.
Janne Pitkäniemi leads the Cancer Epidemiology group. He is also the Director of Statistics at the Finnish Cancer Registry (FCR), Institute for Statistical and Epidemiological Cancer Research, Helsinki. FCR is one the top institutes in the world in population-basedcancer epidemiology and statistical methods in registry based cancer research. The group develops statistical and epidemiological methods related to the estimations concerning time-to-event and familial data ascertained from population-based cancer register. The focus is on cancer burden, survival, co-morbidity and familiality of cancers.