Technology Expertise Networks and Core Facilities Heidelberg
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
Technical Expertise Network: Immune Monitoring
Since its establishment in 2015, the DKFZ/NCT immune monitoring unit has supported numerous clinical trials including >700 patients and continuously expanded its methods portfolio. We currently provide blood and tissue-based immune monitoring to 14 clinical studies, which include Heidelberg IITs as well as external phase I and II studies. These trials include patients with brain, lung, esophageal, colon, breast and skin cancers treated with immune-modulatory antibodies, vaccines, radiation and cellular therapies.
We aim to develop highly customized approaches and are driven by scientific curiosity. At the same time, we utilize a quality management system, including a panel of validated immune assays, to meet GMP and GCLP requirements of selected trials.
Technological innovation is currently transforming immunology. We are leaving behind tedious screening of pre-selected parameters in bulk populations, in favor of high-resolution profiling of immune receptor repertoires, cellular function, cell state and history:
- High parametric flow cytometry (BD FACS Lyric, 12 fluorochrome parameters) for phenotypic and functional parameters provides us with basic information on the cellular composition of blood and tissue samples. We aim to increase multiplexed measurements of fresh samples to preserve the majority of cells for down-stream analysis.
- We measure immune reactivity and antigen specificity using ELIspot, ELISA, Luminex, as well flow-cytometry and sequencing based assays, to reveal e.g. the cytokine profile, the frequency of antigen-reactive cells and/or the receptors involved in antigen-recognition.
- TCR deep-sequencing and discovery: Immune repertoire analysis has emerged as a powerful tool to understand and track immune responses. We perform DNA-based TCR beta-chain sequencing using a commercial kit (ImmunoSeq) and in-house sequencing facilities and are happy to assist DKTK partners in immune-repertoire analysis.
- Single-cell immune profiling: High-throughput barcoded single cell (sc) analysis represents a quantum-leap for immune-monitoring purposes, as it can resolve functionality in the extreme diversity of immune cells and in parallel deliver their antigen-specific receptors. Using the 10x technology, we can obtain information on TCR, transcriptome and/or proteome of individual cells for up to 10.000 cells/sample.
- Strategic combination of functional assays with bulk- and sc sequencing technologies using blood, tissue, expanded T cells or TIL cultures enables the rapid discovery of candidate tumor-reactive receptors that are cloned and undergo in vitro functional validation.