About us

Brief introduction into the activities of the Centre for Clinical Genomics and Personalized Medicine

Background

The Clinical Genomics Center of the University of Debrecen was established in 2001 in order to provide access for the researchers of the University to the novel genomic technologies and to foster academic-industrial partnerships in the field of genomics and personalized medicine.

From a technological point of view in the first period we provided the technology to quantitate gene expression for individual genes and in a whole genome approach. These technologies were shortly complemented with biobanking and high throughput sample processing.

Our most recent technological acquirements are next generation sequencing instruments and tools to investigate functional genomic and epigenetic aspects of gene expression regulation. Our throughput for 2011 is well represented by the number of samples processed on our microarray systems which is close to 600 arrays.

Our facility has a staff of seven post PhD researchers and five technicians.

Our most important instruments are: Illumina HiScanSQ, Affymetrix System, Qiacube robotic systems, Tecan Freedom EVO pipetting System, IPStar epigenetic robotic system, and high capacity bioinformatic server

Since 2011 October we are located in the In Vitro Diagnostic Building having 800 sqm space in a building shared with the Laboratory Medicine and Microbiology Institutes at the Nagyerdei Clinical Campus.

Currently we are involved in several biobanking projects and our partners are leading Hungarian and international pharma companies.

We are committed to provide continuous training for local researchers and we were organizers of two prestigious international practical training programs: the HHMI sponsored training in 2006, FEBS sponsored practical training in 2011.

The scientific director of the unit is Professor Laszlo Nagy, member of the Hungarian Academy of Sciences.

The Genomics Center has expertise in the following areas related to biobanking:

1. Organizing clinical sample collections and processing, in close collaboration with the clinics

Uniform and reliable sample collections are based on well-founded enrollment criteria and standard operating procedures (SOP) for collecting, transporting and processing of samples. Initial phase of the biobanking effort is devoted to establishing the enrollment criteria and SOPs. If needed, the Genomics Center provides training for nurses for more specialized sample collection procedures.

2. Sample processing and storage

The Genomics Center has the infrastructure and expertise to process clinical samples by a variety of techniques, from simple aliquoting of biofluids before storage to more advanced protocols, including: antibody-based cell sorting by MACS, Ficoll or Percoll- based centrifugal separation of cell subpopulations, preparation of cytospin slides, isolation of RNA and DNA, or archiving of solid tissue samples. Depending on the processing protocol and sample numbers, samples can be processed one by one, or in batches by high-throughput methods, using robotics. Samples can be stored at various temperatures; labile samples are stored either at -70°C in ultralow freezers, or in liquid N2 storage tanks at the Genomics Center. Samples are barcoded before storage, and information about the different collections is warehoused in the FreezerWorks software.

3. Research infrastructure

The Genomics Center has 26 m2 laboratory space dedicated for biobanking, a cold room, and a room for ultralow freezers and lN2 storage tank. In addition to standard molecular biology equipment we have the following specialized instruments: five ultralow freezers with CO2 backup and cell-phone-connected alarm system, a lN2 storage tank (storage capacity: 8000 vials), two QiaCube nucleic acid isolation robots, and Tecan pipetting robots for high-throughput sample processing and 96/384-well plate assembly.

Reference:

One of our largest biobanking project: SCHIZO Biomarker project

The aim of the project

The aim of the project is to develop biomarkers and methods to support, rationalize and accelerate the discovery and development of novel drugs for the treatment of psychotic disorders. As a result more effective drugs with fewer side effects than the existing ones can be put on the market.

The project consists of three tasks with the following goals:

1. To establish a disease based biobank (named SCHIZOBANK) collecting both phenotypical and environmental data and biological materials from schizophrenic patients. It will be applied for the identification of genes and genetic variations that influence disease susceptibility. In addition it will be also used to find biomarkers, which speed up the diagnosis of the disease and help monitor the drugs' effect.

2. The aim of this task is to reveal different relations between the symptoms and the treatment of schizophrenia at the molecular level by using the arsenal of the systems biology approach. We will identify biological and clinical predictors (biomarkers) of patient response and adverse side-effect profile during antipsychotic drug treatment.

3. In this task we will determine markers and pathways of the metabolic syndrome adverse effect of antipsychotic in humans, in rodent experimental model systems, as well as in vitro cellular systems. The effect of prototypic antipsychotic drugs will be examined in these models and signatures of drug effects as well as mechanisms of action will be identified.

Members of the consortium

1. UD-GenoMed Medical Genomic Technologies Research and Development and Service providing Ltd.

2. Richter Gedeon Chemical factory Plc.

3. Kripto Research and Development Ltd.

4. University of Debrecen

5. Hungarian Clinical Neurogenetic Society

Sections of work

1. To establish schizophrenia biobank

2. To identify schizophrenia and treatment-related molecular markers

3.1. Metabolic syndrome of the psychiatric disorders patients with AAP treatment: identify marker

3.2.-3.6. Metabolic syndrome of the psychiatric disorders patients with AAP treatment: identify marker: molecular mechanism research

Results

The above-mentioned stages of the professional background of clinical sample collection (quality assurance, determination of methodologies), as well as the infrastructure is completed, and we started filling the biobank. The peripheral blood of schizophrenic patients transcripts, proteomics and metabolomics analysis is in progress, caused by antipsychotic drugs of the side markers of metabolic syndrome, defined rodent samples is also underway.