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).

Scientific Core Facilities and Services Heidelberg

Scientists at the DFKZ and its partner sites can rely on broad portfolio of research infrastructures for their research projects. These include experimental core facilities, data management and IT services. Core facilities are centralized laboratories that operate as user laboratories or as full service units, or both, depending on the technology in question. They offer access to high-end instrumentation, provide scientific and technical advice to users, and are engaged in method development and technology-oriented research. Data management and IT services cover the IT infrastructure demands of the DKFZ and provide also software tools for organizing and handling research data properly.

Below, the DKFZ Core Facilities are listed according to their area of specialty.

Genome, Transcriptome & Epigenome
Next Generation Sequencing (S. Wolf)
Microarray (M. Bewerunge-Hudler)
Single Cell OpenLab (J.-P. Mallm)

Proteome
Proteomics (D. Helm)
Single Cell OpenLab (J.-P. Mallm)
Microarray (M. Bewerunge-Hudler)
Antibodies (I. Hofmann)

Metabolome
Metabolomics (G. Poschet, with Heidelberg University)

Cellular and Preclinical Imaging
Light Microscopy (F. Bestvater)
Electron Microscopy (K. Richter)
Small Animal Imaging (M. Jugold)
Radiopharmaceuticals and Preclinical Trials (I. Kurth)

Cytometry and Screening
Flow Cytometry (S. Schmitt)
Chemical Biology (U.Uhrig, with EMBL)

Whole Tissue Analyses 
Light Microscopy (F. Bestvater)
Single Cell OpenLab (J.-P. Mallm)

Reagents ans Resources for Cancer Resarch
Antibodies (I. Hofmann)
Cellular Tools and Clone Repository (R. Will)
Radiopharmaceuticals and Preclinical Trials (I. Kurth)
Dieter Morszeck Biorepository (S. Röhling)

Animal Services
Center for Preclinical Research (K. Reifenberg)
Tumor Models (N.N.)
Microbiological Diagnostics (K. Schmidt)
Transgenic Service (F. van der Hoeven / B. Armstrong)

Research Data Management 
Omics-IT and Data Management (I. Buchhalter)
OMERO@DKFZ (internal link)

Library & IT Services
Information Technology (C. Galuschka)
Central Library (D. Sitek)