Laboratory of Cytomolecular Genetics (CMG)

Welcome!

The polestar in the research by CMG (Cytomolecular Genetics) group is to mine clinically relevant cancer biomarkers by various microarray techniques and deep sequencing, and adapt the markers found for targeted patient diagnostics and personalized treatment.

Figure 1: From patient to research and back to bedside

Background information of CMG group:

• Location: Haartman Institute, University of Helsinki, Helsinki, Finland
• To contact: Prof. Sakari Knuutila, Laboratory of Cytomolecular Genetics, Department of Pathology, Haartman Institute, P.O.Box 21, FI-00014 University of Helsinki, Helsinki, Finland, email: sakari.knuutila(at)helsinki.fi
• CanGEM (Cancer GEnome Mine): a web-based database for clinical information about tumor samples and microarray data.
• Research group
• Publications since 2002: 182
• Publications in 2011: 14
• Percentage of bicyclists: 100%

Figure 2: Team leader Sakari Knuutila near by the Haartman Institute after snow riding :).

Characteristic of CMG group:

• Systems biology research approaches: from base pairs to chromosomes, from chromatin structure to gene function and gene regulation, from stem cells to differentiated ones, from individual to population and from environmental exposures to diseases
• International research and diagnostics: ongoing EU projects: The European LeukemiaNet, the EuroBoNeT, the EuGESMA COST Action
• Multidisciplinary research: oncology, pathology, microbiology, cytogenetics, molecular genetics, bioinformatics, data base information
• R&D
• Translational research
• Diagnostics service: Transfer research results to clinical practice and develop together with HUSLAB Laboratory of Genetics diagnostic assays for detecting clinically relevant biomarkers in cancers and developmental disorders.
• Research and diagnostics training: post doctoral, doctoral, undergraduate students, medical geneticists and laboratory technicians
• Researcher and student exchanges
• Support of research career of young researchers

What does CMG group offer to you?

• Research collaboration
• Facilities for research visits
• Consultation of cancer cytogenetics and molecular genetics
• Basic diagnostics of molecular karyotyping (aCGH by high throughput platforms) on cancer and mentally retarded people from different kind of cellular material also from formalin fixed and paraffin embedded tissues

Figure 3AB: Microarrays by 240K oligonucleotide based (A) and 1000K SNP-based (B) platforms from a leukemia patient indicate focal chromosome instability at 9p including heterozygous and homozygous losses of numerous genes. (See more details in our recent paper by Usvasalo et al.: Focal 9p instability in hematologic neoplasias revealed by comparative genomic hybridization and single-nucleotide polymorphism microarray analyses. Genes, Chromosomes and Cancer 49:309-318, 2010).

• miRNA profiling by microarray platforms, from paraffin embedded material, too

Figure 4AB: Multidisciplinary research with pulmonarists, pathologists, geneticists and bioinformaticians, as well as international collaboration between our research group and the one in London made it possible to separate histological subtypes of malignant mesothelioma by miRNA profiling and bioinformatics analyses. PCA (principle component analysis) (A) and clustering analysis (B) indicate that sarcomatoid (SA) and deciduoid (DE) differ from normal and epiteloid (EP) / biphasic (BI) subtypes. (See more details: Guled et al. 2009. CDKN2A, NF2, and JUN are dysregulated among other genes by miRNAs in malignant mesothelioma—a miRNA microarray analysis. Genes, Chromosomes & Cancer 48:615-623).

• Connection to the CanGEM database, which provides public access to published results and user-controllable permissions to preliminary data.

Updated 28.2.2012