Sequencing

The services offered by the Next-Generation Diagnostics Unit include joint experimental planning of the individual sequencing project, isolation and quality control of the starting samples (usually DNA or RNA) as well as sample preparation and performance of the actual sequencing. Many standard methods are validated in our laboratory and are performed according to SOP. However, we are also happy to implement individually adapted or new protocols with you.

Furthermore, it is possible to use our sequencing capacities for your own sequencing libraries.

If required, the raw sequencing data can be transferred directly to the Bioinformatics Unit via an established interface and evaluated there with regard to individual questions.

Our offer for preclinical and clinical applications

Classical NGS methods

• Whole transcriptome sequencing (mRNA, totalRNA): gene expression profiling for biological and/or medical questions (e.g. cancers, rare syndromes) as well as translational research
• Amplicon-based sequencing: sequencing of selected genomic regions for precision oncology as well as testing for hereditary diseases
• Genome sequencing / exome sequencing: genome profiling for cancer studies as well as translational research
• Small genome sequencing: targeted or complete sequencing of genomes with low complexity (such as bacteria, viruses or phages)

Advanced NGS methods

• Single cell sequencing and multiomics: transcriptome profiling and parallel detection of surface proteins of single cells. For example, for functional control of therapeutic CARs (e.g. CAR-T cells, CAR-NK cells) and monitoring of therapy success in patients.
• Spatial transciptomics: Spatially resolved gene expression profiling in tissues close to single cell resolution, for example for parallel molecular and imaging characterization of tumor, tumor infiltrating immune cells and tumor microenvironment.

For the control of quantity, quality and integrity of RNA and DNA samples, which can be isolated from various starting materials, the following equipment is available

• DeNovix
• Qubit
• NanoDrop
• BioAnalyzer
• Thermal cycler

Three different instruments are available for performing next-generation sequencing. Depending on the experimental requirements, they allow a flexible number of samples as well as a scalable data output.

• NextSeq 2000, Illumina 
  Application: sequencing of human genomes and transcriptomes as well as single cell sequencing

• MinION, Oxford Nanopore Technologies 
  Application: sequencing of long DNA fragments e.g. for rapid pathogen diagnostics

• MiSeq, Illumina 
  Application: for sequencing of smaller genomes (e.g. bacteria, viruses) and amplicon-based sequencing

Equipment for single cell sequencing preparation

• 10x Chromium Controller
  Application: microfluidic separation and molecular barcoding of cells

• LUNA Automated Cell Counter
  Application: automatic determination of cell counts (living vs. dead)

Our work processes are carried out in accordance with the guidelines of our certified ISO 9001 quality management system.