Cancer Genome Sequencing and Proteome Analysis Platform (CGP)

The major strengths of DKTK`s CGSP is its unique infrastructure and long-standing expertise based on successful projects within multi-institutional initiatives at the highest level, such as the International Cancer Genome Consortium (ICGC) and the International Human Epigenome Consortium. In addition, the platform established and benchmarked internationally referenced bioinformatics pipelines.

Cancer Genome Sequencing Platform (CGSP)

The main aims of the Cancer Genome Sequencing Platform (CGSP) are:

  • To provide an efficient infrastructure for large-scale cancer genome sequencing
  • To create harmonized procedures and common standards for sequencing-based diagnostics within the DKTK.
  • To promote the exchange of expertise and experience related to cancer genome sequencing among the different partner sites.

The central DKTK Sequencing Unit, located in the DKFZ Genomics and Proteomics Core Facility in Heidelberg, is currently equipped with

  • Quality control and analyte extraction
  • Library preparation
  • Next Generation Sequencing technologies
  • Quality control

This central infrastructure is complemented by individual cancer genomics units at the different DKTK sites that provide more focused sequencing technologies, in particular entity-specific gene panel testing, allowing for the targeted molecular profiling of clinical specimens.

Cancer Proteome Analysis Platform (CPAP)

Research into the genetic basis of cancer has been immensely facilitated by genomics, notably whole-genome, whole-exome and RNA sequencing. However, many aspects of molecular cancer research are best studied at the protein level such as the expression levels of oncogenes, the activation status of oncogenic signaling pathways, and the sensitivity of cancer cells to drugs, to name a few. Recent advances in proteomic technology now enable these topics to be studied at an unprecedented qualitative and quantitative scale. Today, many thousands of proteins including several activity-regulating post-translational modifications such as phosphorylation and ubiquitinylation can be quantified across tumors, Patiente Derived Xenograft (PDX)-models and cell lines, leading to a better understanding of the complex molecular events underlying the disease. DKTK establish a Cancer Proteome Analysis Platform (CPAP). encompass world-class expertise over a very broad range of topics The overarching goals of the DKTK CPAP are to bundle this expertise (, to build further capability and capacity and make them available to the five DKTK Programs.

The DKTK partner sites have accumulated a wide range of proteomic expertise in quantification of gene/protein/microRNA expression control, the NFkB pathway and the ubiquitinome secretome profiling, biomarker discovery, FFPE tissue analysis and tumor proteome profiling.

The technical requirements for proteomic research vary greatly depending on the scientific question asked. Therefore, the CPAP is organized in a decentralized fashion to take advantage of the specific expertise and equipment at each DKTK partner site. The main goals of the Platform are: i) to organize and provide scientific services for all DKTK Programs and partner sites for routine applications; ii) to foster scientific collaborations by providing access to specialized proteomic research infrastructure and expertise; and iii) to promote the development and exchange of expertise and know-how.

Coordinators

Prof Dr Benedikt Brors
German Cancer Research Center (DKFZ)

Prof Dr Bernhard Küster
Technische Universität München

Working impressions

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

Cancer cells can be grow under controlled conditions in incubators which allow systematic investigation of oncogenic signaling and intervention with therapeutic drugs

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

Powerful computing is used to store, process and analyse the terabyte scale data that is produced during a proteomic project campaign.

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

The electrospray ion source is the interface between the chromatography system used to separate complete proteomes into more manageable mixtures of proteins and the mass spectrometer which is the central analytical device for the identification and quantification of proteins.

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München

© Bernhard Küster /Technische Universität München