Christian-Albrechts-University Kiel

Christian-Albrechts-Universität zu Kiel
Schittenhelmstrasse 12
24105 Kiel
Germany

http://www.uni-kiel.de

http://www.ikmb.uni-kiel.de

 

Principal Investigator

Prof. Andre Franke

Prof. Andre Franke

Phone +49-431-5974138

Contact

Project Staff

Michael Forster

Software development and bioinformatic analysis
Phone +49-431-5971028

Contact

Institute Presentation

The CAU (http://www.ikmb.uni-kiel.de) is operating a high-throughput genotyping and sequencing core facility. The genotyping and sequencing platforms are built on top of a high-throughput pre-PCR lab and all laboratory processes are monitored by the local laboratory information management system (LIMS). Where applicable, standard operation procedures and automated workflows (e.g. using Tecan pipetting robots) have been developed. CAU uses a fully-equipped Illumina iScan system for applying the Illumina GoldenGate or Infinium technology. GoldenGate custom genotyping panels (384 to 1536plex) could be used for follow-up (genotyping) studies. CAU is currently operating four 96-capillary Sanger sequencers (3730xl from Applied Bio-systems) and six  Next Generation Sequencing machines: 2x SOLiD v4 from Applied Bio-systems, 3x Illumina HiSeq 2000, and 1x Roche 454 GS-FLX Titanium. More than 799 research projects have been completed on these platforms and in 2010 alone yielded more than 10 TB of raw sequence data (plus 90 TB of analysis data). Besides targeted sequencing (several pilot projects ongoing), the CAU has established whole-exome and whole-genome sequencing of case-control collections. To cope with the vast increase in data production and subsequent data processing, large investments were made recently into the IT infrastructure. The applicants have exclusive access to large parts of the high performance computation clusters (HPC) of the University of Kiel (http://www.rz.uni-kiel.de/hpc/rzcluster/). This parallel linux cluster will be used for most analyses and extended through the project. Extensive storage is available through five storage servers that currently offer >290 TB capacity and which are connected to the HPC. In addition, an in-house storage and analysis server (8 node linux cluster with >130 TB storage) is currently being set up at the Institute. A dedicated stand-alone web server provides the general researchers with access to their secondary and tertiary sequencing analysis results.

The CAU will be involved in Networking (WP2, WP4), in Transnational Access (WP8), and Research Activities (WP11). Existing protocols will be improved or novel ones developed for the SOLiD or Illumina platforms. Several enrichment technologies will be benchmarked and SOLiD-compatible or Illumina-compatible protocols developed; focus is made on the performance regarding subsequent SNP, InDel and structural variation detection. Development of analytical tools for categorisation and priorisation of identified variants. We will develop tools to provide the general researcher with powerful data mining procedures. For WP8 we will provide state-of-the-art sequencing and genotyping and particularly bring in clinical expertise, specifically in inflammation barrier diseases and cancer research.