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university of tampere: faculty of medicine and life sciences: research:
Lääketieteen ja biotieteiden tiedekuntaUniversity of TampereLääketieteen ja biotieteiden tiedekunta
Matti Nykter - Computational biology

Computational Biology group develops algorithms and computational models to address biomedical research problems.  The group’s aim is to uncover the molecular basis of human cancers and to generate new avenues for treatment and diagnostics. To reach this goal we integrate both experimental and computational expertise within our research group. We are part of Prostate Cancer Research Center (PCRC) and have set up a brain tumor research program in collaboration with Tampere University Hospital.

Research highlights

Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas
We have previously identified and characterized FGFR3 fusions in glioblastoma. Here we performed FGFR3 immunohistochemistry on tissue microarrays containing 676 grades II–IV astrocytomas and 116 grades II–III oligodendroglial tumor specimens. Fifty-one cases were further analyzed using targeted sequencing. Moderate to strong FGFR3 staining was detected in gliomas of all grades, was more common in females, and was associated with poor survival in diffuse astrocytomas. Strong FGFR3 protein expression is indicative of FGFR3 fusions and may serve as a clinically applicable predictive marker for treatment regimens based on FGFR inhibitors.

Granberg K. et al. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro-oncology, 19(9):1206-1216, 2017.

Earlier publications

Decision support for pathologists: machine learning based image interpretation
Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. Our study shows how machine learning based image interpretation can be used for detecting the cancer hot spots from WSIs. Our method was able to detect metastatic tissue from breast cancer lymph nodes samples with high accuracy (AUC in tumor tissue detection ranging between 0.84-0.91). Based on random forest classification model, we were also able to find a shortlist of top contributing features, providing insight into differences in spatial properties of the tissue types.

Valkonen M et al. Metastasis detection from whole slide images using local features and random forests. Cytometry A, 91(6): 555-565, 2017.

DNA repair gene loss is detectable in circulating tumor DNA
Germline mutations in DNA repair genes have been recently reported in 8 - 12% of patients with metastatic castration resistant prostate cancer (mCRPC). In this study, we performed targeted germline sequencing of 319 metastatic castration resistant prostate cancer patients and showed that patients carrying deleterious germline mutations in genes linked to homologous recombination exhibit attenuated responses to androgen receptor targeted therapy. Using cell-free DNA sequencing, we showed that germline BRCA2 mutations associated with somatic loss-of-heterozygosity in all but one case. These results suggest that mCRPC patients with germline DNA repair defects can be prioritized for more effective therapies using a blood test.

Annala M et al.
Treatment Outcomes and Tumor Loss of Heterozygosity in Germline DNA Repair-deficient Prostate Cancer.
Eur Urol (in press)

Computational Biology Group is in charge for the organization of the international masters education in Bioinformatics at the University of Tampere.

Current sources of External funding: Academy of Finland, Finnish Funding Agency for Technology and Innovation (TEKES), Tampere University Hospital, Cancer Society of Finland, National Institutes of Health (USA), Sigrid Juselius Foundation.

Prostate Cancer Research Center (PCRC)

The PCRC brings together groups from all units of UTA in the campus; BioMediTech, School of Medicine (MED), and School of Health Sciences (HES). Also, Tampere University Hospital, Fimlab Ltd, and a unit from Tampere University of Technology (TUT) are closely affiliated to the research center.

Home page: Prostate Cancer Research Center

Faculty of Medicine and Life Sciences
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