Technologies

The Institute for Pathology has a long tradition in developing novel technologies for the implementation of diagnostic assays. The research unit contributes to this process and applies these and additional technologies to address questions relevant for translational research. Three of these technologies are summarized below. We apply them to our own research projects on a daily basis, but we also offer them for external research collaborations and for supporting the realization of clinical studies.

 

Tissue Microarrays (TMA)

The tissue microarray technology was co-developed and first published by members of our institute in 1998. The establishment of this technology and its application to the large amount of formalin fixed and paraffin embedded (FFPE) tissue samples with clinicopathological information have resulted in numerous publications. In the last 10 years, we constructed at least 400 different TMAs comprising more than 100’000 tissue spots. Due to higher demand in the last years, we equipped our TMA laboratory with the TMA Grand Master, a high-capacity, fully automated TMA construction device that can handle up to 72 FFPE blocks and allows for digital selection and monitoring of the region to punch. Our TMAs are used for in-house research projects, as well as for collaborations with external partners from other universities or pharmaceutical and biotech companies.

 

Next generation sequencing

Diagnostic sequencing (Molekulare Pathologie und Zytologie) is routinely performed in our institute by usage of the next generation sequencing technology. In research, the access and use of this technology has dramatically influenced the design of research projects and clinical studies, since genomes, transcriptomes and epigenomes can nowadays be analyzed in a short time (less than one week). Our NGS laboratory is equipped with three NGS devices (1 IonProton and 2 IonPGMs) as well as with devices for automated library preparation and chip loading. All steps from sample preparation to sequencing are performed in accredited laboratories, commonly used in diagnostic routine. We select and amplify regions of interest for sequencing by application of commercially available gene panels, as well as custom panels specifically designed for current studies. The combination of our professional laboratory staff, data analysis specialists, molecular biologists and pathologists does allow for a versatile and meaningful use of this technology in a clinical and translational research setting.

 

Genomic analyses of liquid biopsies

Our research laboratory has established the methodologies for the genomic analysis of circulating cell-free tumor DNA (cfDNA) from patients suffering from neoplastic diseases. We have set up a robust workflow including cfDNA extraction from plasma or serum followed by NGS with commercially available or specific custom made gene panels. To achieve higher sensitivity (<2% allelic frequency), we have implemented the use of digital PCR. The setup of DNA/RNA extraction from circulating tumor cells (CTCs) and their subsequent genomic analyses are in progress.

 

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