Technology Centre

FIMM Technology Centre develops methods and provides a broad spectrum of biomedical research services to researchers locally, nationally and internationally. In 2015, FIMM Technology Centre operated eight core units with a total of 46 technology experts from diverse educational backgrounds being involved in the operations. Technology Centre offers services in the areas of genomics (sequencing, genotyping, transcriptomics, epigenomics, copy number variation profiling and cell line authentication), high throughput biomedicine (screening of chemical compounds, approved drugs, and siRNA, as well as serum, cell and protein lysate microarrays), metabolomics, digital imaging and molecular pathology, sample processing, bioinformatics, and IT using state-of-the-art technologies.

FIMM Technology Centre operates in close collaboration with the following four Biocenter Finland infrastructure networks: Genome-wide methods, Translational technologies (Drug Discovery and Chemical Biology Platform DDCB, Tissue biobanking: virtual microscopy), Proteomics and Metabolomics and Bioinformatics. It is also strongly involved in three European Research Infrastructure (ESFRI) networks (EATRIS, EU-OPENSCREEN, BBMRI). In 2015, FIMM Technology Centre was supported by the University of Helsinki (Biocenter Finland), the Academy of Finland (EATRIS, BBMRI, EU-OPENSCREEN and FIRI funding for equipment) and the Systems Microscopy Network of Excellence project.

In 2015, the demand for research infrastructure services increased significantly, which was evident in the number of projects, sample amounts and the total revenue in all the units. FIMM Technology Centre offered professional research services in over 600 projects and generated revenue of a 3.2 M €. Over 150 research groups from local, national and international universities and research institutes, as well as from a few companies utilized our services. High Throughput Biomedicine, Genomics and Bioinformatics units increased their production and revenue again in 2015.

 FIMM Technology Centre year 2015 in numbers.

In addition to high quality and high-throughput laboratory services, the Technology Centre offers expertise in project planning, method development, data handling and analysis. In 2015, our staff members were involved in many collaborative research projects with both national and international research groups and were co-authors of many scientific publications solely based on these projects.

As an example, The Drug Sensitivity and Resistance Testing platform (DSRT), developed at FIMM together with High Throughput Biomedicine Unit, played a key part in the recent Nature publication, by Tea Pemovska, Krister Wennerberg and colleagues. DSRT is the most popular assay at the high Throughput Biomedicine unit, and covers with its 527 compounds all approved and many emerging cancer therapeutics, enabling an individualized selection of potentially effective therapies for leukeamia patients. In this study, FIMM researchers, in close collaboration with researchers at Pfizer, identified a previously unrecognized action of a drug called axitinib as a potent inhibitor of the dominant mutation that confers drug resistance to all well tolerated treatments in patients with certain types of leukeamia.

New Technologies and Services in 2015

Digital microscopy and molecular pathology unit is a new service unit launched at FIMM Technology Centre in 2015. It is based on a long-term set up of capabilities as part of research, and infrastructure and technology development projects. The unit started the fee-based whole-slide scanning service beginning of September in 2015 and provides cell- and tissue sample whole-slide scanning, digitization and data storage for local, national and international users. Unit offers wide-field microscope imaging for bright field and fluorescence scanning. During 2015, a total of 1,259 slides were scanned with an average delivery time of less than three days. Currently, the unit has two scanning instruments available: a high-throughput whole-slide scanner (Pannoramic P250 Flash II, 3DHistech) and a high-resolution whole-slide scanner (Axio Imager Z2 + Metasystems VSlide software). During 2016, a new scanner will be purchased to complement the scanning services, and novel services will be developed for histopathology (conventional and multiplexed immunohistochemistry) and image analysis (quantification of protein expression and cell counting).

Digital microscopy and molecular pathology unit was launched at FIMM Technology Centre in September 2015. Reija Randén-Brady coordinates the whole-slide scanning services.

FIMM Technology Centre Sample processing unit operates in the cross roads between the biobank and other research infrastructures providing fast and custom-tailored sample processing for translational research samples arriving from hospitals for molecular profiling. The services produced in 2015 include 225 Ficoll separations of cells from bone marrow and blood, 625 DNA and 263 RNA extractions from various cell types and formalin-fixed samples as well as the quality-control procedures for all of the samples.

 During the year 2015, the Genomics unit launched mouse genotyping by sequencing (GBS) as a new requested service. This new service was implemented in collaboration between the Sequencing and Genotyping Units and utilizes FIMM’s next generation sequencing platforms. The panel currently includes 1,447 SNP markers. It replaced the no longer available Illumina Mouse MD Linkage array previously used for mouse speed congenics analyses in our laboratory. With the new GBS panel, the genotyping is made easier than ever before. The results are delivered in illustrative heterozygosity plots for easy speed congenics evaluation.

Looking into 2016

Novel infrastructure for single cell analytics services

Single cell analytics has huge scientific potential. Overall, analysis of individual cells may provide valuable information on various diseases and developmental processes and also facilitate the discovery of novel cell subtypes.

With the help of the FIRI funding received in December 2015, Infrastructure for Single Cell Capture and Processing aims to develop methods and set up national services for medium to high throughput capture, processing and analysis of individual cells. FIMM will purchase equipment needed for capturing single cells and processing their DNA or RNA for subsequent analysis. Also a post doc researcher will be hired for developing methodology and setting up services. We aim to start the first projects already during the spring 2016.

Single cell services proposed as part of Biocenter Finland activities

 To be able to develop single cell services further, the single cell network has applied for the service to be included among the Biocenter Finland activities. FIMM will concentrate on developing sequencing-based single cell analytics, as well as bioinformatics needed to analyse the results. Pirkko Mattila from Sequencing Unit acts as a coordinator of the network and will carry out the set-up of single cell services together with several other FIMM Technology Centre experts. FIMM-EMBL Group Leader Simon Anders is the chair of the proposed Biocenter Finland Single Cell Network and he will also be responsible for developing new bioinformatics methods for single cell analysis.

Technology Centre