Core Facilities München
© Bernhard Küster/ Technische Universität München
The Core Facility Proteomics at the DKTK Partner site comprises five high-end mass spectrometers, several liquid chromatography systems and terabyte scale computing infrastructure.
The range of supported applications span quantitative protein expression profiling of human and animal tissues, tumors, cell lines and body fluids, dynamic analysis of post-translational modifications, protein-protein interactions, drug target identification, drug mechanism of action analysis and many more. We can offer discovery type proteomic experiments using multidimensional chromatography coupled to the latest Orbitrap technology as well as targeted assays using parallel reaction monitoring. All major quantification workflows are established in the laboratory including SILAC, TMT and a range of label-free analysis. We typically work on the basis of scientific collaboration in which we engage our expertise along the entire path from experiment design through to data acquisition and bioinformatic analysis.
Leukemia Genomics Facility
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Genetic characterisation plays a central role for diagnostics, treatment selection and prognostication in patients with leukemia. In close cooperation with local and DKTK partners, we support DKTK scientists exploring the biology and pathogenesis of leukemia.
Our aim is to develop innovative techniques for leukemia diagnostics. Our location at the Ludwig-Maximilians-Universität München (LMU) in the Department of Hematology and Oncology provides a close collaboration with the clinic and translational research groups. We have access to a large number of well-annotated patient specimens that have been collected at our routine diagnostics laboratory (Laboratory for Leukemia Diagnostics).
MiSeq personal sequencer
Our facility can provide the following services to DKTK-affiliated groups:
Genetic characterization of human tissue specimens (primarily peripheral blood and bone marrow) using a variety of approaches including
- Metaphase and molecular cytogenetics
- Conventional molecular genetics (Sanger sequencing, fragment analysis and qPCR; various assays established for recurrent mutations in hematopoietic neoplasms)
- Targeted next-generation sequencing (established panels of recurrently mutated genes in myeloid and lymphoid neoplasms)
- Whole-exome and whole-genome sequencing
- Single-cell genotyping
Analysis of recurrent gene mutations in 664 AML patients using targeted sequencing
Our main areas of research focus on the following topics
- Genetic characterisation of myeloid neoplasias
- Evaluation of novel prognostic and predictive markers in leukemia
- New therapeutic targets in leukemias
- Identification of markers for minimal residual disease (MRD)
- Research on clonal evolution of leukemia
Core facility members: Prof. Dr. Karsten Spiekermann, Dr. Klaus Metzeler, Dr. Tobias Herold, Dr. Philipp Greif, Dr. Nikola Konstandin, Dr. Sebastian Vosberg, Sebastian Tschuri
Xenograft mouse model of acute leukemias
The Core Facility “Xenograft mouse model of acute leukemias” studies primary patients´ tumor cells growing in mice, performs preclinical treatment trials and molecular studies on basic disease biology.
In vivo bioluminescence imaging (BLI) allows reliable and sensitive follow-up of preclinical treatment trials
The core facility offers:
- engrafting and amplifying primary tumor cells from patients with ALL or AML as patient-derived xenografts (PDX) in mice
- biobank of re-transplantable PDX samples for in vitro studies, >50 for ALL and >10 for AML
- genetic engineering in PDX (GEPDX) cells for overexpression of transgenes
- preclinical in vivo treatment trials monitored by bioluminescence in vivo imaging
- quantifying treatment responses as early as 4 days after treatment
- covering all disease stages including minimal residual disease
- focusing on challenging sub-populations such as dormant stem cells
Characteristics of AML PDX samples that were established within the first DKTK funding period