Genomics and Proteomics Core Facility

Biomedical research increasingly depends on global molecular analyses of normal and diseased phenotypes. These include qualitative as well as quantitative investigations at the genome and proteome levels that are required to eventually achieve a mechanistic understanding of disease or to identify novel markers for diagnosis, prognosis or prediction. Central infrastructures are key components in such research processes as these provide access to state-of-the-art technology platforms that are operated by dedicated personnel, thus overcoming redundant implementation of often demanding technologies within an institute. Along these lines, the Genomics and Proteomics Core Facility of the DKFZ covers mostly four major areas and provides professional services.

• The genomics part of the facility operates one of Europe’s largest next-generation sequencing units. We sequence within several national and international cancer genome projects, on top of a variety of individual in-house projects. Gene expression profiling, genotyping and methylation analysis is carried out using array-based technologies, providing high throughput at reasonable cost. All these applications generate molecular profiles at the level of nucleic acids and provide information about alterations in the disease context.
• Technologies in mass spectrometry and NMR are provided for qualitative and quantitative analysis of proteins, protein modifications and small molecules. These applications allow views on the activation states of signaling proteins in cancer pathways and help to generate mechanistic knowledge of tumor diseases.
• In the field of functional genomics we generate monoclonal antibodies targeting cancer-relevant proteins, some of which are now used in diagnosis. Cell lines stably expressing recombinant proteins from isogenic loci in the respective genomes are generated to assess phenotypes of proteins and mutants in in vitro as well as in vivo systems, e.g., xenograft mouse models (collaboration with animal facility). In addition, we offer the customized generation of retro- and lentiviral particles and viral transduction of cell lines including the complete Biosafety approval and documentation.
• The central infrastructure of the GPCF offers assisted access to costly instruments, and distributes the human ORF clone resource of the international ORFeome Collaboration for recombinant expression of encoded proteins, e.g., in isogenic cell lines.

We carry out joint projects with scientific groups of the DKFZ to implement latest technologies that shall serve the needs of science. Our mission is to always enable application of state-of-the-art technologies. On top of providing full or assisted access to services we are involved in the teaching program of the DKFZ, and organize tech-talks, seminars and practical courses where we inform interested scientists, predocs and technicians on the technological background of applications.

Many different services are integrated within the individual groups listed above. The Microarray Unit performs expression profiling of mRNA and miRNA, Genotyping and genome-wide methylation analysis. High-Throughput  sequencing is offered and monoclonal antibodies, stable isogenic recombinant cell lines and a clone and vector repository are available. Additionally we provide booking of central GPCF equipment like Real Time PCR machines, sample preparation robots or SilverQuant scanning systems or the wetlab wiki, which allows you to share and discuss protocols with your colleagues at DKFZ.