DKTK Core Facilities: Genomics

Cancer Genomics Core Facility Frankfurt

The DKTK Cancer Genomics Core Facility was set up at the DKTK location in Frankfurt/Mainz in 2015 in response to rapid developments in the field of tumour genetics and next-generation sequencing (NGS). The unit is equipped with an Illumina MiSeq sequencing system and is located within the unit at the Department of Medicine II (Haematology/Oncology) at University Hospital Frankfurt.
The following methods/techniques are currently available:

• Quality control of NGS libraries (e.g. before sequencing on HiSeq sequencing systems)
• Targeted sequencing of tumour samples (targeted/amplicon sequencing)
• Analysis of genetic screens

Large sequencing projects, including exome sequencing, full genome sequencing and RNA sequencing, can be carried out in collaboration with the Genomics & Proteomics Core Facility at the DKFZ.

4C-PMU Unit (Cancer Center Unit for personalized medicine) Berlin

The 4C-PMU is a joint cancer sequencing initiative of the Charité Comprehensive Cancer Center (CCCC), DKTK, and the Laboratory of Molecular Tumor Pathology (MTP), and the molecular pathology unit at the Institute of Pathology. The sequencing unit houses two Ion Torrent PGM systems, one Ion Chef and one Illumina MiSeq system (Fig. 1). Sequencing approaches are focused on customized and commercially available gene panels permitting in-depth analysis of heterogeneous cancer samples. Specific gene panels were developed for the following cancer entities: colon cancer, head and neck carcinoma, lymphoma, neuroendocrine carcinomas, breast cancer and leukemia. Panels for ovarian cancer, pediatric tumors, and melanoma and are still under development. Two Droplet Digital PCR systems and two StepOnePlus Real-Time PCR systems were installed for the validation of the sequencing data. The analysis of liquid biopsy samples is currently being developed for head and neck cancer. The 4C-PMU performs on request companion diagnostics based on NGS analysis within clinical trials organized at the CCCC.
Bioinformatics analysis is done as a community effort conducted mainly by local DKTK groups, and supported by the Computational Modeling Group at IRI (Humboldt University) and the informatics unit (CUBI) at the Berlin Institute of Health (BIH).

Genomics and Proteomics Heidelberg

The DKFZ Genomics and Proteomics Core Facility (GPCF) is a central research infrastructure providing DKTK members access to sophisticated key technologies that serve the need of biomedical science and offering high quality solutions at reasonable costs. Trained and dedicated personnel ensure highest quality and reproducibility of our services. Services are processed according to the "first come - first served" principle.

The GPCF technology portfolio mostly covers the following areas:

• The genomics part of the facility operates one of Europe’s largest next-generation sequencing units offering Illumina HiSeq and MiSeq technologies, the latest Illumina Hi-Seq X-Ten platform and the NovaSeq und NextSeq technologies. GPCF performs WGS, WGBS, WES, ChIP-seq, mRNA-seq, smallRNA-seq etc. within several national and international cancer genome projects (e.g., INFORM, DKTK), in addition to a variety of individual in-house projects. The unique Illumina HiSeq X-Ten platform for whole genome sequencing, which was funded by DKTK and established in the years 2014-2015 allows whole genome sequencing of more than 8,000 patients per year.

  Gene and miRNA expression profiling (Illumina, Agilent, Affymetrix), genotyping (Illumina, Affymetrix) and methylation (Illumina MethylationEPIC BeadChip) analysis is carried out using array-based technologies. Moreover, an array-based kinase activity profiling service is established. At the beginning of January 2019, the High Throughput Sequencing-Unit and the Microarray applications for clinical analysis were accredited according to the international standard DIN EN ISO/IEC 17025.

• The proteomics section provides technologies for analyzing proteins, protein modifications and small molecules by state-of-the-art mass spectrometry and NMR in a qualitative and quantitative manner.
• In the field of functional genomics the GPCF generates monoclonal antibodies on demand, some of which are by now used in diagnostics. The service covers the production of monoclonal and polyclonal antibodies, as well as the non-GMP production and purification of antibodies on a larger scale for preclinical studies.
  Isogenic cell lines stably expressing recombinant proteins or shRNAs from a particular genomic locus are generated e.g., to assess phenotypes of proteins and mutants in in vitro as well as in vivo systems, e.g., in xenograft mouse models. Furthermore, a lenti/retrovirus transduction service, which includes filing the application, risk assessment, cell line transduction and the complete safety documentation, is established.
• The central Infrastructure of the GPCF offers assisted access to several costly instruments (e.g., qPCR- and ddPCR-system) being utilized by a number of scientific groups with help of an online booking system, and it further distributes the human ORF clone resource of the international ORFeome Collaboration (>17,000 human genes) for recombinant expression of encoded proteins, also in isogenic cell lines.

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

GPCF Homepage: www.dkfz.de/gpcf