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.

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NGS at a glance

At the 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. Several sample preparation protocols can also be fully automated using the Biomek FX laboratory automation workstation (Beckman Coulter) at the Fraunhofer IGB.


Sequencing 

Depending on the scope of the application, the choice of NGS technology determines sequence depth and read length of each sequencing run. In this context, once a (c)DNA library has been prepared, it is sequenced either on the Illumina HiSeq2500 with very high read depth but shorter fragments (up to 2 x 250 bases), or on the Roche GSjunior, which has far lower read depth but can process longer sequences (up to 700 bases).


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.

Next-generation diagnosis of infections

The diagnosis of infectious diseases is based mainly on microbiological techniques. The cultivation of pathogens in the laboratory, however, is a time-consuming process and some pathogens cannot be cultivated at all or only under special conditions.

For this reason, we develops innovative molecular methods for pathogen diagnostics based on molecular analyses of the genetic information of pathogens.

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Reference projects

Non-coding RNAs as biomarkers

Biomarkers for CPOD and prostate cancer, based on the molecule class of non-(protein)-coding ribonucleic acids (ncRNAs), are investigated within the “Ribolution” project supported by the “Fraunhofer-Zukunftsstiftung” (Fraunhofer Future Foundation).

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Characterization of microbial populations in biogas production

Within the BMBF-funded project “GOBi”, we use metagenome and metatranscriptome analyses to characterize microbial communities in silages and biogas fermenters. These insights may lead to optimized processes in biogas production through targeted manipulation of microbial composition.

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ERA-HyPerIn

The focus of the project HyperIn, funded within the ERA-Net Program, lies in the integrated approach for the identification of novel P450-enzymes with the potential for targeted conversion of fine chemicals within industrial processes. Therefore, de-novo sequencing procedures of non-characterized bacteria and fungi followed by a functional annotation of the genomes, as well as identification of active genes via gene expression analyses, are some aspects of the project which are addressed by the Functional Genomics group.

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