RNA Biomarker

The unit is primarily concerned with searching for and validating new diagnostic and prognostic RNA biomarkers for a number of different diseases. It has a range of molecular methods available for the screening and validation process in line with GLP, e.g. next generation sequencing, microarrays, and PCR-based methods. An additional focus lies on accompanying diagnostics, which is viewed as a key step towards personalized healthcare. The team develops specific tests (e.g. for diagnosing cancer) to help them reach this ideal goal.

Well-established Standard Operating Procedures are in place for next generation sequencing (NGS) involving short RNAs (e.g. microRNAs) and long RNAs (e.g. mRNAs, long noncoding RNAs), as well as microarray analyses.

The validation of identified markers is also well established and implemented using analytical qRT-PCR. Furthermore, a fully automated facility for high-throughput qRT-PCR with an integrated nano-dosing system (I-DOT) is being developed for biomarker validation together with Fraunhofer IPA.

In the RNA Biomarker Unit, sequencing protocols for both long and short RNAs from a range of patient materials are completed in a standardized manner with the aid of Illumina sequencing systems (MiSeq; Ultra-High-Throughput Sequencing System HiSeq 2500).

Alongside transcriptome sequencing, DNA capture sequencing and DNA amplicon sequencing are also carried out. The unit's infrastructure facilitates an extremely broad spectrum of possible applications and study sizes that goes beyond the above-mentioned technologies.

The project "RIBOLUTION – integrated platform for the identification and validation of innovative RNA-based biomarkers for personalized medicine" represents a research alliance supported by the Fraunhofer-Zukunftsstiftung (Fraunhofer Future Foundation).

New RNA biomarkers are identified and their diagnostic application validated for selected diseases using comprehensive, genome-spanning screening techniques. RIBOLUTION also includes so-called noncoding RNAs, which were recently discovered as a large reservoir of potentially valuable medical biomarkers.

Biomarkers are being sought that function as diagnostic indicators to reveal diseases or predict their course or response to therapy. In addition, the process of biomarker screening will be optimized and perfected by RIBOLUTION with the aid of technical innovations.

• Illumina sequencing platform Hiseq 2500 (Ultra-High-Throughput Sequencing System)
• Illumina sequencing platform Miseq
• Microlab STARlet (Hamilton, automatically prepares samples for sequencing)
• Qiacube (semi-automated extraction and purification of nucleic acids)
• Microarray scanner (Agilent, Affymetrix)
• Perkin Elmer Labchip GX (to determine the quality of nucleic acids, can be integrated into automation)
• Perkin Elmer Labchip DS (to quantify nucleic acids, can be integrated into automation)
• Agilent Bioanalyzer (to determine the quality of nucleic acids and proteins)
• Nanodrop (to quantify nucleic acids)
• Qubit 2.0 (extremely sensitive fluorometric quantification of specific nucleic acids)
• Covaris M220 Focused-ultrasonicator™ (nucleic acid shearing, active paraffin removal from FFPE tissues)

• Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biology. 2014 Feb 10;15(2):R34. DOI dx.doi.org/10.1186/gb-2014-15-2-r34.