Biomedical Research; Biomedical Technology; Computational Biology; Epigenomics; Genomics; Hematology; High-Throughput Nucleotide Sequencing; Rare Diseases; Single-Cell Analysis; Stem Cells
- Biomedical Sequencing Facility (BSF)
- Medical Epigenomics Lab
The Medical Epigenomics Lab (http://www.medical-epigenomics.org/) combines large-scale epigenome analysis with stem cell biology and computational modeling, in order to better understand and treat cancer and other diseases. We collaborate with biologists and clinicians at the Medical University of Vienna and internationally, aiming to advance precision medicine through technological innovation. Specific research interests include:
1. Epigenomics. We perform large-scale epigenome mapping in order to dissect the dynamics of cancer development and emerging drug resistance. This work is part of the European BLUEPRINT project and the International Human Epigenome Consortium.
2. Technology. Exciting biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell protocols, nanopore sequencing, CRISPR, and epigenome editing.
3. Bioinformatics. New algorithms and advanced computational methods allow us to accurately infer epigenetic cell states from large-scale datasets, in order to reconstruct the epigenetic landscape that controls cellular differentiation and reprogramming.
4. Diagnostics. Using large-scale DNA methylation mapping, bioinformatic prioritization, and functional characterization, we strive to develop clinically relevant biomarkers for informing personalized cancer therapy.
Techniques, methods & infrastructure
The Biomedical Sequencing Facility (http://biomedical-sequencing.at/) is Austria’s first and leading center of expertise for next generation sequencing in biomedicine. Under the leadership of Christoph Bock, the BSF contributes to biomedical research and whole genome medicine in Vienna, Austria, and internationally. The BSF also performs the genome sequencing and analysis for Genom Austria (http://genomaustria.at/), which is the Austrian Personal Genome Project (http://www.personalgenomes.org/austria). The BSF is equipped with the latest technology for large-scale genome research, including three Illumina HiSeq sequencers (including the latest 3000/4000 platform) for production sequencing; an Illumina MiSeq sequencer for technology development and gene panels; a PerkinElmer Sciclone NGS (pre-PCR) and Zephyr (post-PCR) robotics system supporting 96-well automated library preparation for RNA-seq, RRBS, and ChIP-seq; a Silicon Biosystems DEPArray and a Fluidigm C1 for single-cell sequencing. The BSF is also part of the Oxford Nanopore early access program. It is supported by a powerful scientific computing cluster upgraded annually to keep pace with steeply increasing data generation. The BSF’s mandate includes a focus on technology development, contribution to study design and bioinformatic data analysis, as well as training and teaching best practices in sequencing technology and genomic medicine.
- CINOCA - Co-infection as a cause of ovarian cancer (project partner) (2013)
Source of Funding: EU, FP7-ERA-NET on Human Infectious Diseases (Infect-ERA)
- High-throughput dissection and reprogramming of epigenetic drug resistance in leukemia (2013)
Source of Funding: OeAW (Austrian Academy of Sciences), New Frontiers Group
- EpiMARK - An integrated approach for epigenetic risk assessment and biomarker development for breast cancer in prospective cohorts (project partner) (2012)
Source of Funding: EU, FP7-ERA-NET on Translational Cancer Research (TRANSCAN)
- BLUEPRINT - A Blueprint of Haematopoietic Epigenomes (project partner) (2011)
Source of Funding: EU, FP7-HEALTH-2011
- Schmidl, C. et al., 2015. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nat Meth, 12(10), pp.963-965. Available at: http://dx.doi.org/10.1038/nmeth.3542.
- Farlik, M. et al., 2015. Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics. Cell Reports, 10(8), pp.1386-1397. Available at: http://dx.doi.org/10.1016/j.celrep.2015.02.001.
- Bock, C., 2012. Analysing and interpreting DNA methylation data. Nature Reviews Genetics, 13(10), pp.705-719. Available at: http://dx.doi.org/10.1038/nrg3273.
- Bock, C. & Lengauer, T., 2012. Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer, 12(7), pp.494-501. Available at: http://dx.doi.org/10.1038/nrc3297.
- Bock, C. et al., 2011. Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell, 144(3), pp.439-452. Available at: http://dx.doi.org/10.1016/j.cell.2010.12.032.