Genomics & Proteomics Core Facility - DKFZ

(Source: Deutsches Krebsforschungszentrum (DKFZ) / T. Schwerdt). The use of the material in connection with the EU project EASI Genomics is authorized by the DKFZ.  A transfer of the image material to third parties is permitted only after prior consultation with the DKFZ Communications Department. Commercial use is prohibited.

The DKFZ Genomics & Proteomics Core Facility GPCF was established in 2006 as a central Research Infrastructure providing a portfolio of strongly requested state-of-the-art technologies to the DKFZ scientific community and offers professional services in specialized units mostly in the areas of genomics,  proteomics, functional genomics and infrastructures. The genomics part of the facility operates one of Europe’s largest next-generation sequencing units. The Sequencing Unit is involved in several national and international cancer genome projects, in addition to a variety of individual in-house projects. Gene expression profiling, genotyping and methylation analysis is carried out using array-based technologies.

In conjunction with the genomics applications bioinformatics services offered, GPCF serves the groups of DKFZ and the National Center for Tumor Diseases (NCT), the National Cancer Consortium (DKTK) and beyond. GPCF is a collaboration partner in a large number of projects within personalized medicine: DKTK, Heidelberg Center for Personalized Oncology (HIPO;  https://www.dkfz.de/en/hipo/index.html), Precision Oncology Program (POP), and Individualisierte Therapie für Rückfälle von bösartigen Tumoren bei Kindern (INFORM). A number of large-scale projects strictly depend on the quality services provided, like the PedBrain project (http://www.pedbraintumor.org/) of the International Cancer Genome Consortium (ICGC). GPCF has a staff of 52, 15 holding PhD degrees and more than half are women.

The GPCF (S. Wiemann/S. Wolf/M. Brück) will provide Transnational Access to whole genome and whole genome bisulphite sequencing (X-ten), exome sequencing and RNA sequencing. 

Technical equipment and infrastructure

The GPCF Sequencing Unit operates 10 Illumina HiSeq X, 2 NovaSeq,  2 HiSeq 4000, 3 HiSeq 2000, 2 NextSeq 550, and 2 MiSeq sequencing instruments. Applications provided include DNA Sequencing, ChIP-Sequencing, RNA-Sequencing and Bisulfite Sequencing. Lab automation is realized with 5 Agilent Bravo pipetting robots (sample QC, pre-PCR, post-PCR).

Sequencing services (WGS on HiSeq X, RNA Seq on HiSeq 4000, WES on HiSeq 4000,) are accredited according to the international standard DIN EN ISO/IEC 17025 which defines the competence requirements for testing and calibration laboratories.

Services