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Institute of Diagnostic Virology (IVD)

Laboratory for Applied Bioinformatics and Sequencing of Viral Genomes and Transcriptomes

The rise of high-throughput sequencing enabled scientist to access huge amounts of sequencing data within minimal analysis times on a moderate budget. Therefore, high-throughput sequencing of the second generation, also known as next-generation sequencing (NGS) has become a key tool in nearly all projects dedicated to life sciences. However, post-processing and analyzing these huge amounts of data is still a mayor bottleneck as size, complexity and structure of sequencing data requisite the use of specialized bioinformatics software.

Task

The Laboratory for Applied Bioinformatics establishes streamlined and automated workflows for analysis of sequencing data, with respect to the peculiarities of viral genomes. One central aspect is therefore the application and connection of already existing bioinformatics software in order to generate high-quality viral genomes and functional annotations. Especially for complex DNA virus, such as Herpesviruses, a functional annotation of coding regions is only accessible via the viral transcriptome. The laboratory is therefore using specialized sequencing methods that allow targeted sequencing of viral messenger RNA (mRNA) in order to achieve synergistic effects of combining genomic and transcriptomic data.

Furthermore, the laboratory is actively supporting the organization, implementation and analysis of gene expression studies. These studies use sequencing methods in order to quantify the effects of a stimulus, e.g. viral infection or active chemical compound, on the expressed transcriptome of the underlying model in relation to untreated controls. As a result, the effects caused by the stimulus can be traced back to transcriptional activation or shutdown of single genes and functional correlated metabolic pathways. In order to conduct these expression-based analysis using non-model organism, the laboratory is constantly developing workflows for the assembly and annotation of de novo transcriptomes.

Finally, existing bioinformatics workflows and programs are maintained and improved by the Laboratory for Applied Bioinformatics. In order to conduct and organize high-throughput sequencing experiments the laboratory is working in close contact to all working groups within in the Friedrich-Loeffler-Institutes and especially the Laboratory for NGS and Microarray Diagnostics.

Main research subjects and projects

  • Sequencing of viral genomes, functional annotation and phylogenetic classification
  • Comparative gene expression experiments
  • Analysis of host gene expression signatures associated with persistent foot-and-mouth disease virus infection in cattle for advanced diagnostics and therapy
  •  „Transcriptional landscaping“ as tool for functional annotation of complex DNA viruses
  • Identification and characterization of exogenous genes in complex DNA viruses (host DNA/RNA capturing by viruses)
  • Establishment of improved phylogenetic methods for classification of viruses based on their genetic repertoire

Other

The laboratory wasaccredited in 2003 and is subtyping BVDV samples that have been tested positive by the NRL for BVD/MD, using RT-PCR and sequencing. Furthermore, the laboratory is organizing and conducting the first-generation sequencing (Sanger) and fragment length analysis for all other laboratories at the Friedrich-Loeffler-Institutes (Riems) using a Genetic Analyzer 3130xl and 3500.