Functional genomics via next-generation sequencing (NGS)

Sequencing technologies – the next generation

Next-generation sequencing (NGS) describes a novel technology in nucleic acid analysis. In contrast to conventional sequencing techniques, it enables the simultaneous sequencing of hundreds of millions of DNA fragments. These high-throughput or parallel sequencing technologies have opened up entirely new dimensions in nucleic acid analysis and revolutionized countless areas of life sciences research.

In our research group, we use NGS technologies for a wide range of challenges with a scientific as well as an application-oriented focus. Projects cover, for example, de novo sequencing of industrially or medically relevant bacterial and fungal strains, analyses of transcription profiles, identification of relevant genes, e. g. for an early diagnosis of tumor diseases, and screening for biomarkers for diagnosis.

We are especially proud of our group’s ability to offer the complete workflow from sample preparation to sequencing up to bioinformatics analyses.

From wet lab to dry lab: complete sample analysis

At Fraunhofer IGB, we have established a three-step process that encompasses the various steps in sample preparation and sequencing in the laboratory as well as subsequent bioinformatics analysis.

Sample preparation

To use the next-generation sequencing technology, the samples must be processed differently depending on the starting material and the scientific problem that is addressed in the experiment. For example, genomic DNA from unknown organisms is used for de-novo genome sequencing while a variety of RNA populations (mRNA, smallRNA, ncRNA) can be examined in transcriptome analyses.

DNA/RNA extraction by cryo-grinding for different materials encompassing for example:

  • fungi, bacteria, blood, fermenter as well as animal, human and plant tissues

 

Repertoire of application-specific protocols:

  • DNA: whole genome shotgun (WGS), amplicons, enrichments.
  • RNA: polyA+, ncRNA, strand specific sequencing, rRNA and/or globin depletion
  • full automation using the Biomek FX pipetting robot available for several protocols
  • individual establishment of new protocols or fast and flexible adaption of established protocols

Sequencing

Depending on the scope of the application, the choice of NGS technology determines sequence depth and read length of each sequencing run.

Genome sequencing (DNA-seq)

  • de-novo
  • resequencing
  • metagenomes

Transcriptome sequencing (RNA-seq)

  • mRNA
  • small RNA
  • nc RNA
  • microbial RNA
  • metatranscriptomes

Amplicon sequencing (AMP-seq)

  • rDNA
  • exome
Beladung der Illumina Hochdurchsatz-Sequenzierplattform für die Sequenzierung.

Bioinformatics

By means of our high-performance IT infrastructure optimized for NGS, the sequenced raw data can then be bioinformatically evaluated for a variety of different applications like gene expression anaylsis, genome assemblies and annotations or metagenome analyses. Beyond that, we developed the GeneScapes genome browser for visualization of sequencing data.

  • De-novo assembly
  • annotation of de-novo assemblies using in-silico or, if desired, experimental methods
  • mapping and variance calling
  • RNA-seq including detection of differential gene expression
  • metagenome and metatranscriptome analyses
  • biomarker screening

Please contact us for an individual offer

 

Please contact us for your personal offer  

sequencing [at] igb.fraunhofer.de

 

Flyer Next Generation Sequencing

From wet-lab to dry-lab.