In the research area Immunology we focus on the description and research of the human adaptive immune system.The human adaptive immune system plays a vital role in the detection of potential pathogens, diseases that are difficult or impossible to cure, such as various types of cancer and autoimmune diseases. We also rely on the functionality of our immune system during transplantation processes.One of the main tasks here is the identification and description of the components and signal pathways which lead to a specific immune reaction or which differ in diseased and supposedly healthy individuals. This makes an important contribution to the explainability of various diseases and the development of new, innovative therapies.The latest technologies in molecular biology generate large amounts of data that have to be analyzed efficiently. We here mainly deal with the analysis of genetic data. This includes the analysis of gene expressions, database analyses and the identification of mutations. The main focus is on diseases such as leukemia, but also organ rejection reactions and infectionswith various pathogens such as Helicobacter pylori.Since 2012, we have been developing the ImmunExplorer software, which enables algorithms for the analysis of the human immune repertoire, the immunoglobulins and T-cell receptors, from blood and tissue data. An extensive expansion and continuation of ImmunExplorer, namely ImmunoDataAnalyzer, will be published soon in 2020. In close cooperation with our partners at MedUni Vienna, AKH Vienna, University of Salzburg and the Hospital of the Barmherzigen Brüder we strive to advance the research area and intensify national and international cooperation.
|2019||Roman Reindl-Schwaighofer, Julia Vetter, Johannes Weinberger, Susanne Schaller, Andreas Heinzel, Guido Gualdoni, Constantin Aschauer, Kira Jelencsics, Karin Hu, Stephan M. Winkler, and Rainer Oberbauer:||T-Cell Repertoire of Tissue Infiltrating T-cells at Time of Rejection||American Transplant Congress 2019|
The ImmunoDataAnalyzer (IMDA) provides various methods for analyzing immunological next generation sequencing (NGS) data, focused on immunoglobulins (IG) and T cell receptors (TCR). IMDA is especially built for first interpretations and quality control of TCR or IG repertoire data analysis. Several aspects based on CDR3 and V(D)J genes are calculated, evaluated, and additional visualizations are provided.
IMDA constructs TCR and IG repertoire data from raw NGS reads and facilitates descriptive data analysis and comparison of immune repertoires. The IMDA workflow focus on quality control and ease of use for non-computer scientists. The provided output directly facilitates the interpretation of input data and includes information about clonality, diversity, clonotype overlap as well as similarity, and V(D)J gene segment usage. IMDA further supports the detection of sample swaps and cross-sample contamination that potentially occurred during sample preparation. In summary, IMDA reduces the effort of a usually required for immune repertoire data analysis by providing an automated pipeline for processing raw NGS data into immune repertoires and subsequent evaluation. The implementation is open-source and available on http://bioinformatics.fh-hagenberg.at/immunoanalyzer/.
Susanne Schaller MMSc
Susanne Schaller MMSc
Julia Vetter MSc
Prof.(FH) PD DI Dr. Stephan Winkler
2017 - present
University of Applied Sciences Upper Austria, Hagenberg, Austria
Department for Nephrology, Medical University of Vienna, Austria