In-vitro diagnostics

The development and application of innovative methods concerning next-generation sequencing, as well as synthetic biology, are the main focus of the Functional Genomics research group headed by Dr. Kai Sohn. These methods provide the basis for the identification of biomarkers for personalized diagnostics of various clinical indications and the molecular analysis of infection processes, but also for the characterization of microorganisms in industrial biotechnology. Furthermore, methods for the qualitative and quantitative characterization of complex microbial metagenomes and metatranscriptomes are developed and applied to diagnostics and environmental biotechnology.

To this end, a complete workflow was established in our group to provide an 'all-in-one' solution from sample preparation to bioinformatics. Our automated sample preparation, next generation sequencing and high performance computing workflows are available for cooperation and joint research projects, as well as research projects of industrial clients.

Fields of activity and technologies

  • NGS-based diagnostics
  • Precision diagnostics and biomarkers
  • Microbiomics
  • Environmental genomics
  • Bioinformatics
 

Next-generation diagnostics

Despite good medical standards, there are still inadequate diagnostic procedures for many diseases to this day. We use next-generation sequencing technology to identify new biomarkers for improved diagnosis of, for example, prostate cancer, COPD or infectious diseases.

 

Precision diagnostics of microbial resistance and environmental monitoring of resistance development

Microbial resistance against antibiotics is a worldwide problem. Next generation sequencing opens up new possibilities for detecting resistance as well as for monitoring resistance from a large number of biological samples.

 

Genomics for white and environmental biotechnology

We also use NGS genome analyses to characterize microorganisms for industrial biotechnology. In addition, we develop methods for the qualitative and quantitative detection of complex microbial metagenomes and transcriptomes for environmental biotechnology.

Next Generation Sequencing Services

The Functional Genomics group has established a three-step process to handle inquiries for high throughput sequencing. This process, consisting of sample preparation, next generation sequencing and bioinformatics, is highly adaptive due to various established preprocessing and sample preparation protocols, as well as fast and flexible bioinformatics.

These characteristics enable a variety of applications, like de-novo genome and transcriptome sequencing of biotechnological production strains or human pathogens or meta-genomics and meta-transcriptomics, as well as facilitating early diagnosis of infectious and cancerous diseases.

Equipment

QIAcube (Qiagen)

  • automated sample preparation using Qiagen kits
  • up to 12 samples

 

Axio Observer.Z1 microscope (Zeiss)

  • ApoTome
  • fluorescence microscopy

 

BioAnalyzer 2100 (Agilent)

  • quality control, RNA and DNA quantification

 

Biomek Fx (Beckman Coulter)

  • automated sample preparation
  • individually programmable protocols

 

GS Junior (Roche)

  • pyrosequencing with long read length of up to 700 bp

 

HiSeq2500 (Illumina)

  • high throughput sequencing 
  • various kits for sample preparation to address different scientific problems

 

HPC

  • high-performance computing cluster with four computing units (100 CPUs, 770GB RAM)
  • backup via on-site tape library

Sample preparations

 

  • NA/RNA extraction established for various materials
    • Fungi and bacteria from pure cultures or directly from their biocenosis
    • Animal and plant tissues (incl. FFPE)
    • Blood, stool and environmental samples

 

  • Comprehensive repertoire of specific protocols available
    • DNA-Seq: whole genome shotgun (WGS),165 amplicons, enrichments
    • RNA-Seq: polyA+, small RNA, ncRNA, strand specificity, rRNA- and/or globin-depletions
    • Automation on Biomek FXP

 

Established NGS-technologies 

Sequencing with lllumina NextSeq 2000 Read length Reads/
Flowcell
Capacity/
Flowcell
Advantages
High output run mode 2 x 150 bases 1,1 bn 330 gb Universally applicable, high throughput
Rapid run mode 2 x 150 bases  400 Mio 120 gb Rapid data delivery time 

 

Information materials

 

Brochure “Next-Generation Sequencing”

Scientific publications