Next-Generation Diagnostics

Analysis methods for the biological marker validation and test development

The unit has a special focus on the continuous establishment of new and the adaptation of existing analysis methods for particular questions of biomarker validation. The work primarily involves next-generation sequencing, microarrays analyses as well as PCR-based processes. Solutions for the development of marketable test systems are moreover in development, in close collaboration with the RNA Biomarker Unit in order to precisely define the requirements for the respective biological marker groups.

Next-generation sequencing

The Next-Generation Diagnostics Unit uses the HiSeq 2500 System as well as the MiSeq System from Illumina for next-generation sequencing. These sequencing platforms are applied in a broad spectrum of methods. Aside from performing genome- and transcriptome-wide sequencing, the unit’s focus is on establishing and further developing special sequencing protocols, for instance for DNA / RNA capture sequencing, amplicon sequencing, identifying SNPs and mutations as well as for characterizing small genomes. The outstanding connection to the Bioinformatics Unit subsequently permits a highly qualitative evaluation of this sequencing data.

Microarray analyses

A microarray platform from Agilent is available for the highly parallelized performance of gene expression analyses. Apart from the microrarrays for mRNA, Exon, miRNA and ncRNA analyses offered by Agilent, user-defined microarrays for special questions can be designed in collaboration with the Bioinformatics Unit.

Interaction studies

The Next-Generation Diagnostcs Unit has built up an extensive range of methods to obtain insights into the cellular interactome. The SILAC method has been successfully employed for protein-protein interaction studies. Furthermore, chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP) have been conducted to examine the interplay of proteins with DNA or RNA. Likewise protocols were established to identify RNA-binding partners to RNA, at the DNA and protein level, which currently are especially being used in the search for new ncRNA-binding partners.