University of Tartu, Estonia
University of Tartu (est. 1632) is one of the oldest universities in Northern and Eastern Europe and a leader of research in Estonia. UT has seen a rapid research impact increase and was recently ranked in first 400 by THE World University Rankings 2011-2012. With the national initiatives that have highlighted the ICT and Biotechnology as strategically most important areas, UT is well positioned with strong educational and research activities in both.
The Estonian Biobank (with official name Estonian Genome Center , University of Tartu (EGCUT)) is one of the leading European population based biobanks – it has samples from 5% of adult population of Estonia in total of 52,000 men and women. Collected DNA, plasma and white blood cells are stored in liquid nitrogen. An extensive database is linked to the biobank comprising clinical and life-style characteristics and information on incident diseases. GWAS data will be available from >10,000 individuals and whole-exome sequencing data from >100 subjects by the end of 2011. EGCUT is in active cooperation with biobank consortia P3G and BBMRI (ESFRI). EGCUT received an ISO 9001:2000 certificate in 2003 and has successfully renewed it since.
The Center of Translational Genomics (CTG) established in 2011, focuses on the development of an unique and universal database based on the Estonian Biobank, where genetic variation, genome transcription and epigenetic alterations are described in detail (association analysis, gene expression profiling, eQTL mapping, linear modeling , DNA methylation analysis etc.) together with the characterization of full proteomes (content, modifications and concentrations) and metabolomes (final products of metabolism) as a direct result of the previous processes. The CTG initiative broadens the biobank by incorporating many more research groups and PIs, including bioinformatics, statistical genetics, etc.
The Bioinformatics and IT research group (BIIT) lead by Prof. Jaak Vilo at Institute of Computer Science is another fine example of UT commitment towards highly multidisciplinary biomedical and ICT research at University of Tartu. BIIT research group focuses on data mining and efficient algorithms for biomedical data analysis. Among the highlights are the gene expression, functional genomics, systems biology and machine learning studies and tools. Recently, Estonia joined the small group of countries to have signed the MoU for joining the ELIXIR ESFRI project, with the infrastructure collaborative node proposal from University of Tartu.
Profile of staff members
1) Prof. Andres Metspalu, M.D, PhD – Director of Estonian Genome Center, University of Tartu
2) Erkki Leego, MSc – IT Director of Estonian Genome Center, University of Tartu
3) Prof. Jaak Vilo - Head of the BIIT Research Group, Head of the Institute of Computer Science
Five publications relevant to the project
1) Comprehensive catalog of European biobanks.
Wichmann HE, Kuhn KA, Waldenberger M, Schmelcher D, Schuffenhauer S, Meitinger T, Wurst SH, Lamla G, Fortier I, Burton PR, Peltonen L, Perola M, Metspalu A, Riegman P, Landegren U, Taussig MJ, Litton JE, Fransson MN, Eder J, Cambon-Thomsen A, Bovenberg J, Dagher G, van Ommen GJ, Griffith M, Yuille M, Zatloukal K. Nat Biotechnol. 2011 Sep 8;29(9):795-7. doi: 10.1038/nbt.1958
2) The role of a bioresource research impact factor as an incentive to share human bioresources
Cambon-Thomsen A, Thorisson GA, Mabile L, Andrieu S, Bertier G, Boeckhout M, Cambon-Thomsen A, Carpenter J, Dagher G, Dalgleish R, Deschênes M, di Donato JH, Filocamo M, Goldberg M, Hewitt R, Hofman P, Kauffmann F, Leitsalu L, Lomba I, Mabile L, Melegh B, Metspalu A, Miranda L, Napolitani F, Oestergaard MZ, Parodi B, Pasterk M, Reiche A, Rial-Sebbag E, Rivalle G, Rochaix P, Susbielle G, Tarasova L, Thomsen M, Thorisson GA, Zawati MH, Zins M; BRIF workshop group.
3) Quality, quantity and harmony: the DataSHaPER approach to integrating data across bioclinical studies
Isabel Fortier, Paul R Burton, Paula J Robson, Vincent Ferretti, Julian Little, Francois L'Heureux, Mylène Deschênes, Bartha M Knoppers, Dany Doiron, Joost C Keers, Pamela Linksted, Jennifer R Harris, Geneviève Lachance, Catherine Boileau, Nancy L Pedersen, Carol M Hamilton, Kristian Hveem, Marilyn J Borugian, Richard P Gallagher, John McLaughlin, Louise Parker, John D Potter, John Gallacher, Rudolf Kaaks, Bette Liu, Tim Sprosen, Anne Vilain, Susan A Atkinson, Andrea Rengifo, Robin Morton, Andres Metspalu, H Erich Wichmann, Mark Tremblay, Rex L Chisholm, Andrés Garcia-Montero, Hans Hillege, Jan-Eric Litton, Lyle J Palmer, Markus Perola, Bruce HR Wolffenbuttel, Leena Peltonen, and Thomas J Hudson. IJE Advance Access published on September 2, 2010. doi:10.1093/ije/dyq139 PDF. Nat Genet. 2011 Jun;43(6):503-4. PDF
4) Hundreds of variants clustered in genomic loci and biological pathways affect human height.
Lango Allen H, Estrada K, Lettre G, ....... Kaplan RC, Metspalu A, North KE, Schlessinger D, Wareham NJ, Hunter DJ, O'Connell JR, Strachan DP, Wichmann HE, Borecki IB, van Duijn CM, Schadt EE, Thorsteinsdottir U, Peltonen L, Uitterlinden AG, Visscher PM, Chatterjee N, Loos RJ, Boehnke M, McCarthy MI, Ingelsson E, Lindgren CM, Abecasis GR, Stefansson K, Frayling TM, Hirschhorn JN. Nature. 2010 Oct 14;467(7317):832-8. Epub 2010 Sep 29.
5) Genetic structure of Europeans: a view from the North-East.
Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, Toncheva D, Karachanak S, Piskácková T, Balascák I, Peltonen L, Jakkula E, Rehnström K, Lathrop M, Heath S, Galan P, Schreiber S, Meitinger T, Pfeufer A, Wichmann HE, Melegh B, Polgár N, Toniolo D, Gasparini P, D'Adamo P, Klovins J, Nikitina-Zake L, Kucinskas V, Kasnauskiene J, Lubinski J, Debniak T, Limborska S, Khrunin A, Estivill X, Rabionet R, Marsal S, Julià A, Antonarakis SE, Deutsch S, Borel C, Attar H, Gagnebin M, Macek M, Krawczak M, Remm M, Metspalu A. PLoS One. 2009;4(5):e5472. Epub 2009 May 8.