Uppsala University

Uppsala Universitet, Department of Medical Sciences

Uppsala Universitet, Department of Medical Sciences
Entrance 70, 3rd floor, research Dept 2
SE75185 Uppsala
Sweden

http://www.medsci.uu.se

Principal Investigator

Prof. Ann-Christine Syvšnen

Prof. Ann-Christine Syvšnen

Phone +46-18-6112959

Contact

Institute Presentation

Uppsala University (UU) (http://www.uu.se) is one of the oldest universities in Europe. It is a large university with nearly 50,000 students and educational programs in all disciplines. Uppsala University was recently funded by the Swedish government to establish a Life Science Laboratory in Uppsala (LSLU). This new laboratory will combine technology platforms and research programs to perform outstanding research in molecular biomedicine. The LSLU Genomics platform is the largest facility for new generation sequencing and SNP genotyping in Scandinavia and has two years of experience from providing access to NGS sequencing applications to a large number of scientists. Currently the SNP technology platform (http://www.genotyping.se) and the genome center in Uppsala (http://www.genpat.uu.se/facilities/genome_center/) that constitute the Genomics platform of LSLU are equipped for new generation sequencing (NGS) with two Genome Analyzer IIX (Illumina) and two SOLiD (ABI) instruments, and at least one additional instrument will be installed. A large storage and analysis system of 2000 cores, 4 TB RAM, and 500 TB of storage space has been established in collaboration with the Uppsala center for high-performance computing. The LSLU Genomics platform is also well equipped for SNP genotyping on a wide size range, using BeadArray technology (iSCAN, Bead Station 500GX, Illumina) for large-scale and genome-wide genotyping and the BeadXpress and SNPstream systems for medium- and small scale genotyping and routinely performs Sanger sequencing (ABI 3730XL). LSLU hosts strong research groups in comparative genomics and in technology development and has a focus on genomic research on cancer, cardiovascular and inflammatory diseases. The Genomics platform will contribute to the project by providing access to NGS by the Solexa- and SOLid technologies, including resources for data analysis and storage. LSLU will also perform SNP genotyping in the areas of cancer, inflammatory diseases and domestic animal genetics. Research and development activities at LSLU will target allele-specific gene expression, sequencing template preparation and data analysis for NGS and use of domestic animals as models for human diseases.

In WP2, UU will participate in harmonisation efforts regarding SNP genotyping on all scales (1 Ė 106 SNPs per sample, CNVs and DNA methylation), and all applications of sequencing using Illumina and SOLiD technology by sharing protocols and by implementing standard best-practice operating procedures agreed on by the consortium. Via the Swedish bioinformatics infrastructure (BILS) and the Uppsala center for high-performance computing (UPPMAX) the UU centre is linked to the European infrastructure for biological information (ELIXIR). Networks with EMBL-EBI are already in place via ELIXIR and other EU-funded projects to harmonise data exchange formats. These activities will be continued and extended in WP4.

The BILS initiative is a coordinated national Swedish bioinformatics infrastructure that will provide sustainable bioinformatics support for life science researchers in Sweden. BILS matches international efforts, of which ELIXIR is the most prominent, and makes it possible for Swedish researchers to efficiently utilise these resources. Furthermore BILS aims to coordinate the activities at various sites in order to provide front-line research-based support to all Swedish life science groups. These activities will be implemented in WP4.

Scientists at our centre are actively involved in BBMRI and other EU FP6 and FP7-projects: Specifically key scientists from our Genomics platform participate in ENGAGE, PROCARDIS, CARDIOGENICS, LUPA, EUROSPAN. These activities will be further developed in WP5.

We will organise a practical course on new generation sequencing technology (WP6).

The involvement in WP8 will include

  • Flexible SNP genotyping on all scales (low numbers of DNA samples and high number of SNPs, low number of SNPs and high number of patient samples).
  • Genomic studies of acute lymphoblastic leukaemia: Re-sequencing of regulatory genomic regions including epityping and ChIP and RNA sequencing, data integration