Microarray analysis
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Mission Our aim is to untangle the genetic background of diseases with public health importance using new biochip and bioinformatics tools. We aim to detect polymorphisms predisposing to complex diseases, to monitor genetic risk profiles formed by these polymorphisms in epidemiological study samples and to explore cellular changes in such diseases with experimental and computer assisted methods. |
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Science We are a novel unit, founded at the beginning of 2001, but have been studying genetics of complex diseases with our collaborators already for a decade. To provide potential for studying genetic background of complex diseases, we are developing and applying new methods, such as SNP microarrays and mass spectrometer based SNP (Single Nucleotide Polymorphism) genotyping methods, for monitoring multiple SNPs simultaneously in large study samples. Additionally, we test and utilize novel biochips, intended for gene expression profiling and gene copy number analyses, in order to identify factors predisposing to complex diseases and to monitor differences at the cellular level. We make extensive use of bioinformatics software and algorithms, which we also develop ourselves, the main focus areas being in sequence analysis, microarray data analysis as well as database systems for storaging and analysis of large molecular biology datasets. The bioinformatics unit collaborates with many research groups, both in the Department of Molecular Medicine as well as other groups in the Biomedicum Helsinki. The bioinformatics unit is also responsible for the Biomedicum Bioinformatics Unit, a bioinformatics core-facility for all the researchers in the Biomedicum Helsinki as well as for their collaborators. Currently over 200 researchers are using the services of the Biomedicum Bioinformatics Unit for bioinformatics analysis. The research topics of the bioinformatics unit are the regulation of transcriptional activity both in humans as well as in certain other model organisms. The research is based on experimental data, obtained from e.g. microarray analysis. By utilizing the whole genomes of the studied organisms, combined with e.g. transcription factor binding site as well as polymorphism analysis, we aim to model the causes leading to the studied, heritable diseases. The main research targets of the microarrays unit are multiple sclerosis (MS) and osteoarthritis (OA), and we work in close collaboration with research groups studying cardio-vascular diseases, mental health disorders and discus degeneration. Genome wide scans were performed for both MS and OAs and several loci showing evidence for linkage were identified in Finnish population. Now we aim to restrict the loci further in order to identify genetic variation(s) predisposing to MS and to OA. Our goal is also to study cellular events behind the diseases by motoring differences in gene expression profiles. Microarray unit functions as a part of the Biomedicum Biochip Center, a microarray core unit. The main focus of Biomedicum Biochip Center is research and technology development for post-genomic era biomedical research, but it also provides access to its capabilities via service and research contracts. Research group Janna Saarela, M.D., Ph.D. Most important publications Hu G, Modrek B, Riise Stensland HM, Saarela J, Pajukanta P, Kustanovich V, Peltonen L, Nelson SF, Lee C: Comprehensive Genomic Mapping and Functional Characterization of Single-Nucleotide Polymorphisms in Coding Regions of Human Genes. Pharmacogenomics J 2002, 2:236-242 Koli K, Saharinen J, Karkkainen M, Keski-Oja J. Novel non-TGF-beta-binding splice variant of LTBP-4 in human cells and tissues provides means to decrease TGF-beta deposition. J Cell Sci 114:2869-78, 2001 Nikali K, Saharinen J, Peltonen L. cDNA cloning, expression profile and genomic structure of a novel human transcript on chromosome 10q24, and its analyses as a candidate gene for infantile onset spinocerebellar ataxia. Gene 299:111-5, 2002 Penttinen C, Saharinen J, Weikkolainen K, Hyytiainen M, Keski-Oja J. Secretion of human latent TGF-beta-binding protein-3 (LTBP-3) is dependent on co-expression of TGF-beta. J Cell Sci 115:3457-68, 2002 Petrova TV, Makinen T, Makela TP, Saarela J, Virtanen I, Ferrell RE, Finegold DN, Kerjaschki D, Yla-Herttuala S, Alitalo K: Lymphatic endothelial reprogramming of vascular endothelial cells by the Prox-1 homeobox transcription factor. EMBO J 2002, 21:4593-4599 Reunanen K, Finnila S, Laaksonen M, Sumelahti ML, Wikstrom J, Pastinen T, Kuokkanen S, Saarela J, Uimari P, Ruutiainen J, Ilonen J, Peltonen L, Tienari PJ. Chromosome 19q13 and multiple sclerosis susceptibility in Finland: a linkage and two-stage association study. J Neuroimmunol 2002, 126:134-42 Saarela J, Schoenberg Fejzo M, Chen D, Finnilä S, Parkkonen M, Kuokkanen S, Sobel E, Tienari PJ, Sumelahti M-L, Wikström J, Elovaara I, Koivisto K, Pirttilä T, Reunanen M, Palotie A, and Peltonen L. Fine mapping of a multiple sclerosis locus to 2.5 Mb on chromosome 17q22-q24. Hum Mol Genet 2002, 11:2257-2267 |
Additional information  MD., PhD. Janna Saarela e-mail: firstname.lastname@ktl.fi Links: Biomedicum
Bioinformatics Unit Molecular Medicine Sequencing Laboratory
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