EATRIS-CZ brings small, medium, and medium-large sequencing and genotyping projects a step closer to reality. Despite the buzz about the low price of getting genetic information, starting a sequencing or genotyping project requires initial investment in millions of Euros, continuous education of staff not only in the wet part of laboratory work but also in bioinformatics, and uninterrupted stream of samples to keep instruments running. In many cases, outsourcing or collaborative research may be the most reasonable solution.
Support of research/drug development projects
Within EATRIS-CZ infrastructure, we can offer services using a dozen of real time thermocyclers including 1536-wells format and droplet digital PCR (Bio-Rad QX200). Moreover, Affymetrix microarray device (Human Gene- and Exon- level expression, miRNA profiling, FFPE OncoScan, HD Cytoscan) and two next-generation sequencing platforms from Illumina (MiSeq, HiSeq) are installed there, with an access to NovaSeq platform.
The supported applications include
- SNP genotyping
- Amplicon sequencing for metagenomic studies
- Targeted sequencing of formalin fixed paraffin embedded (FFPE) samples
- Transcriptome sequencing
- Exon and/or whole genome sequencing
- Targeted detection of cytosine methylation by pyrosequencing and/or massively parallel sequencing
- miRNA and gene expression profiling
Other types of services/analyses offered
- Chromosomal microarrays (CMA)
- Constructing of DNA FISH probes for designated genes/chromosomal areas
- Fluorescent in situ hybridization (FISH)
- Genotyping, SNPs
- High Resolution Melting Analysis (HRM)
- Many types of PCR including ddPCR
- Circulating tumor cells detection and characterization
- Human papillomavirus (HPV) detection and full genotyping of high-risk and low-risk HPV genotypes
- Triage testing of HPV-positive women by methylation test
EATRIS-CZ proteomics facilities feature a comprehensive set of analytical instruments to cover a broad range of proteomic analyses:
Orbitrap based mass spectrometers Elite and Fusion (Thermo Scientific) for discovery proteomics, QTrap 5500 (ABSciex) for protein quantitation and validation by single/multiple reaction monitoring (SRM/MRM). The facilities also offer an access to two MALDI-TOF UltrafleXtreme (Bruker Daltonics) systems.
Except of mass spectrometers, proteomics facilities offer Quadra3 liquid handling workstation (TOMTEC Life Sciences) for solid phase extraction, 1D, 2D, DIGE scanner Typhoon (GE), recombinant protein production and purification instrumentation NGC-Discover,
chromatography system (Bio-Rad) available to expedite a high-volume sample preparation and analysis.
The instrumentation is supported by data management and complex analyses systems that are administered by the cooperating bioinformatics & IT support staff.
Proteomics facilities of EATRIS-CZ partner institutes are able to perform a broad scale of experiments including protein identification and quantification in samples ranging from single
gel bands to whole cell lysates, serum or other biological fluids. Quality control of your samples and LC/MS method development can be done as well.
Support of research/drug development projects
- Protein identification, discovery, quantitation (labelled, label-free), SILAC, FAS
- Biomarker discovery, validation, SWATH, SRM, MRM, glycocapture
- Identification of protein post-translational modifications
- Immunoaffinity pull-down experiments, molecular targets identification
- Mass spectrometry data analyses
- Consultations, trainings
Advantages and options EATRIS-CZ proteomics facilities can bring to your research
- Access to a broad scale of high-end proteomic equipment including Orbitrap, MALDI-TOF,
- Q-TOF and other mass spectrometers connected with nano-LC
- Isotope labeling of proteins not affecting their function and behavior
- Seamless transition from cell-culture to tissue or serum experiments
- Precise targeted quantification with isotope labeled internal standards
- Robotic liquid handling reducing variability
- Both discovery and validation phase can be performed
- Advanced knowledge and methodic support
Biological samples and accompanying patient data are necessary for the development of any new drug or a diagnostic assay and consequently for advancing biomedical research in the context of personalized medicine.
EATRIS-CZ closely collaborates with another medical research infrastructure - European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), providing strong support for translational research projects. Generally, the process of sample collection is marked with close collaboration between patients, surgeons, pathologists, researchers, and biobank personnel. Thus, obtaining a coherent cohort of clinically characterized samples may be behind reach of academic centers without direct contact to teaching hospitals.
Support of research/drug development projects
- EATRIS-CZ members provide direct access to samples from tumor collection that include:
- DNAs (more than 15,000 samples from 8,000 patients)
- RNAs (more than 4,000 samples from 3,000 patients)
- FFPE slices (more than 40,000 samples from 10,000 patients)
- Cryosamples (about 5,000 tissue samples from 1,000 patients with lung, brain, colorectal, breast, lymphatic node, ovary, testicle, prostate, and bone marrow diseases)
- Tissue samples fixed in RNA later (parallelly collected with tissue cryosamples)
- Other tissues samples through appropriate material transfer agreements
Collaborating facilities also provide infrastructure for the storage of frozen and deep-frozen samples, mostly from cancer patients. Among other technologies, the facilities offer capacity in liquid nitrogen cryosystems from Lineq equipped with Kesai alarm systems. Mowden -80 °C cryosystems are also available, and are equipped with CryoData2, Innova U725, and COMET software.
Partner institutes of EATRIS-CZ provide expertise and infrastructure for various types of analysis as well as for acquisition, storage and distribution of complex datasets. Experienced staff members can offer an overlapping expertise in IT infrastructure, programming, web/database management, data mining, statistics, bio/cheminformatics and can consult and assist in study design, implementation, and analysis, or develop new software tools to support your research activities. In addition to standard equipment and common software resources, computing infrastructure of the EATRIS-CZ institutes includes current generation of cluster, which is composed of 43xCPU nodes with Intel Xeon E5-2650 (2x in each node) and 20xGPU nodes with Nvidia Tesla M2090, totally 2016 logical CPU cores, 24x 300 GB + 276x 3TB.
Support of research/drug development projects
- Preparation of design of clinical trials and laboratory experiments (determine sample size, specify analysis plan)
- Conduct statistical analyses and provide statistical support to researchers in appropriate reporting of results
- Perform virtual screening of your libraries with proprietary models predicting cytotoxicity
- Drug design and in silico optimization of compound properties, e.g. ADME, off-target activity, etc. using various computational tools (machine learning, pharmacophore, molecular docking, molecular dynamics, etc.)
- Provision of expertise on the collection, organization, analysis and interpretation of genomic, proteomic and other biological data
- Provision of cheminformatics support for high-throughput screening program including annotation of compounds in the library, analysis of structure-activity relationships and identification of mechanism of action
Available unique software tools and databases
- ClinData - software solution for collecting of clinical and laboratory data on patients included in various research projects and clinical studies (see https://clindata.imtm.cz).
- PreClinData - software solution for collecting and statistical analyses of preclinical data included in various research projects. (see https://preclindata.imtm.cz).
- MedChemBio portal of medicinal and biological chemistry (see http://medchembio.cz/)
- Claire — system for reliable detection of protein variants from tandem mass spectra of proteome (see https://claire.imtm.cz/)
- Decryptor — web-accessible software for identification of mutant and polymorphic proteins from standard MS/MS data (see http://decryptor.imtm.cz/)
- SPCI – software for automated building, validation and interpretation of quantitative structure-activity relationship models (https://github.com/DrrDom/spci)
- Psearch – software for automated building and validation of 3D ligand-based pharmacophore models (https://github.com/meddwl/psearch)
EATRIS-CZ can offer an access to high throughput screening and high content analysis platform – one of the largest academic installations worldwide, providing screening and high-volume biology data on a broad diversity of assays and detection systems. The described HTS platform is industry strong, modular and flexible, and allows testing in BSL3 and BSL2+ environment, screening in combination with ionizing radiation (X-rays), mass spectrometry, high content analysis and others. The screening assays provide leads for downstream drug research and development.
The HTS/HCA screening platform is based on a state-of-art robotic system provided by HighResBiosolutions Ltd. The system consists of three robotic arms, automatic incubators, liquid handlers for microliter and nanoliter volumes, sealers, de-sealers, centrifuges and readers for fluorescence, luminescence, absorbance and ionizing radiation. Also integrated with the system are wide-field or spinning disc confocal microscopes (Operetta, Yokogawa CV7000) equipped with software tools for image analysis and data evaluation. A critical part of the robotic system is the automatized chemical library, containing more than 110 000 compounds.
Support of research/drug development projects
In the field of uHTS/HCA and chemical biology/genetics, EATRIS-CZ offers cooperation in collaborative and contractual R&D projects, including tests of biological activities of small molecules.
Available tests focus on
- Cytotoxicity (non/cancer, resistant cell lines)
- Primary human normal and diseased cells
- Cell cycle analysis (fixed and live cells)
- Phenotypic screens using HCA
- Cytoskeleton modulation/integrity
- DNA, RNA, protein synthesis
- DNA damage/repair activity, screening in combination with X-ray radiation
- Protein-protein and protein-nucleic acids interactions
- G-protein coupled receptor activity (adenosine, cannabinoid and opioid receptors)
- Intracellular calcium flux assay
- cAMP production upon modulation of adenylyl cyclase activity by G-protein coupled receptors
- Mapping the most significant signaling pathways (eg. Hedgehog, Wnt, p53, KRAS, RAGE) via phosphorylation and reporter
- Screening of demethylating agents using an in-house developed cell line
- Custom made biochemical tests
- Antimicrobial activity in G+/G- strains including drug resistant bacteria, mycobacterium strains, yeasts, filamentous fungi,
- viruses and parasites under BSL2 and BSL3 conditions
- Cellular 3D culture models (cytotoxicity, reporter studies, etc.)
Development and validation of homogenous mix-and-measure assay (384-well and 1536-well format) in tight collaboration with the users for:
- Fluorescence polarization
- Fluorescence intensity
- Fluorescence resonance energy transfer (FRET), ALPHA-Screen, LANCE
- Time resolved Fluorescence (TRF)
- High Content Screening
- Identification of new molecular target or new assay approach
- Validation of assay on provided by customer or commercial chemical libraries (Lopac1280, Prestwick, Enzo)
- Support in analysis of HCS data
- Custom scripts for image analysis on Columbus, Acapella, MathLab and ImageJ
- Availability of broad spectrum of reporter cell lines
- Hit and Lead profiling and preclinical development of selected drug candidates
EATRIS partners institutes’ facilities can provide preclinical in vivo efficacy models for numerous diseases, including neurology, oncology, pharmacokinetic, toxicology and metabolic studies. They are also poised to customize preclinical pharmacology and consulting services to speed up a development of your drugs. Preclinical studies at the facilities have also utilized species of laboratory animal models (including GMO animal models) in SPF conditions.
Experts from our partner animal facilities can administer test agents into rodents via any route of administration and perform surgical techniques or procedures with special imaging and analysis capabilities for all specialized and/or custom programs.
Support of research/drug development projects
The researchers can guide you through your basic or translation research projects, select appropriate animal models, design research practices, conduct high-quality in vivo studies, and generate customized study reports.
Pharm / Biopharm
In vivo toxicology studies are intended to assess the onset, severity, and duration of toxic effects, their dose dependency and degree of reversibility (or irreversibility). Within EATRIS-CZ partner animal facilities, in vivo toxicology studies can encompass dosing regimens from acute (single dose) to chronic (multiple doses). Several routes of exposure (e.g. oral, intravenous, intramuscular, topical, etc.) can be accommodated and multiple species of rodents are available. The full complement of toxicology evaluations is available, either through in-house resources or through strategic partnerships with external vendors. These evaluations include biochemistry (clinical chemistry), hematology, urinanalysis, histopathology, bioanalysis and toxicokinetics. Pharmacokinetic (PK) and toxicokinetic (TK) analyses are key activities of early drug development. PK and TK studies provide useful and required information which informs no effect levels (NOEL), human equivalent doses (HED), and pharmacokinetic/pharmacodynamic (PK/PD) drivers. Carrying out pharmacokinetic studies enables the determination of PK parameters such as AUC, clearance, volume of distribution, half-life, Cmax, and Cmin.
In Vivo Cancer Studies
The preclinical oncology studies provide highly customizable in vivo compound evaluation, including studies combined with irradiation, to help evaluate novel anticancer therapies. Studies are conducted from traditional xenografts to advanced humanized mouse models of cancer. This area includes subcutaneous human tumor xenografts, syngeneic tumor grafts, orthotopic engraftment, patient-derived xenografts, tumor cell lines in membrane tubes (Hollow Fiber).
The employees partner animal facilities have experience and expertise in testing an efficacy of novel antimicrobials in bacterial and fungal infectious animal models (e.g. rat model of infected skin ulcer, murine model of bacterial keratitis, mouse peritonitis/sepsis model, murine model of bronchopulmonary, aspergillosis, etc.).
EATRIS-CZ also provides an access to equipment and experts trained in behavioral neuroscience tests (e. g. locomotor activity, anxiety, habituation, cognition, test on behavioral models).
Studies involving models of neurodegeneration
Having experience in work with neurodegenerative disease models, the researchers can also help you with the development of optimal therapeutic strategy, with selected Alzheimer disease models readily available.
Multimodal imaging comprises advanced non-invasive techniques (e.g. PET, SPECT, CT, US, optical) for studying of dynamic biological processes within living animals. To better understand the progression and treatment of diseases, multimodal imaging uses cutting edge technologies allowing quantitative 3D imaging of tracers. It provides data on the kinetics and biodistribution of studied compounds in various animal models. Precise information on the biodistribution profile of the drug is one of the crucial requirements for the future success in the drug development. The state-of-art multimodal imaging systems allows imaging of various kinds of tracers in all types of small animal models (e.g. rat, mouse) and even in models of isolated organs.
Support of research/drug development projects for EATRIS-CZ users
- Multimodal imaging of tracers in given time points
- Evaluation of disease progression or treatment response over time
- Very high resolution and sensitivity resulting in superior image quality
- Rapid multimodal acquisition and reconstruction
- Powerful quantification and dynamic analysis option
- 3D output images combining the data from several imaging modalities
- Longitudinal studies on the same animal
- Possibility of 3D animation outputs
- Biodistribution data output as continuous record in given time period
- Detection of compounds labeled by a wide range of radionuclides
Other advantages and options multimodal imaging can bring to your research
- Assessing the efficacy of your novel drug candidate
- Tracking of physiologic and structural changes together in vivo
- Monitoring of disease progress and drug distribution, delivery and therapeutic response
- Enhancing the efficiency and accuracy of preclinical studies
- Reducing time and costs for the translation
- Powerful approach for characterizing your drug candidate in vivo in preclinical studies
In the field of regulatory compliance, EATRIS-CZ can guide you through a range of necessary procedures, help with documentation and administration, setting standard operating procedures (SOPs) and staff training. Moreover, our partners can also provide capacity in accredited laboratories to accelerate the clinical development of your projects.
- Prototype testing in a controlled laboratory setting in compliance with the ISO 10993-1 and ISO 14155 standard, as well as local regulations and the Declaration of Helsinki
- expertise in assessment and revision of the clinical evaluation documents of the manufacturer or researcher
- assessment of clinical documentation, specifically Clinical Evaluation Reports, Instructions for Use, Risk Analysis Reports, Post-Marketing Clinical Follow-ups and Post-Marketing Surveillance Reports and their compliance with the requirements of European and Czech legislation, harmonized and international standards (EN ISO 14155:2011, EN ISO 14971:2012)
- Project management
- Complex support of clinical research in accordance with legislative requirements and current recommendations
- Regulatory and legislative activities
- Support in the legislative aspects of clinical research
- Provision of insurance of the clinical trial, processing of the Clinical trial agreements with hospitals and private health clinics
- Preparation of the documentation for the clinical trial approval/notification application to regulatory authorities and ethics committees
- Submission of the clinical trial application to regulatory authorities (RAs) and ethics committees
- Submission of the necessary documents to the RA (SÚKL), ethics committees, or other RAs
- Study documentation and site preparation activities
- Preparation and regular update of the clinical trial related documents – protocols, Informed consent forms, Investigator brochures etc. Support with preparation of the internal guidelines and documents of the trial sponsor - SOPs, monitoring plan, Investigational product operation manual, Lab manual
- Study feasibility evaluation, selection of the eligible study sites with regards to the target study population
- Clinical trial monitoring
- Ensuring pre-study visits, initiation visits, regular monitoring visits, close-out visits as per the monitoring plan and in accordance to the study protocol. Cooperation in the wide variety of therapeutic areas
- Training of clinical research associates and site staff as per protocol, GCP training
- Statistics, data management, CRF (case report form)
- Support in the area of planning and design of clinical studies
- Design and production of the electronic CRFs
- Data management activities, including queries resolution
- Consultation and Production of the statistical plan, Statistical data processing
- Pharmacovigilance, medical and safety monitoring
- Support in collection, detection, assessment, monitoring, and prevention of adverse effects
- Support for the correct safety events reporting
- Medical monitoring of the clinical trial (services of study physician)
- Expert safety monitoring of the safety events, data safety monitoring boards
- Submission of the Request of extradition the certificate GLP to regulatory authorities and legislative activities
- Submission of the necessary documents to SÚKL, or else other regulatory authorities,
- Preparation of the documentation for non-clinical studies and Request of extradition the certificate GLP to regulatory authorities and ethics committees,
- Ensuring of agreements with partners and suppliers.
- Test facility management
- Ensuring non-clinical studies accordance with legislative requirements and actual recommendations
- Appointment as Head of test facility, Quality assurance manager and Study director to ensure accountability for the conduct of non-clinical studies
- Trained and experienced staff familiar with the test procedures, standards and systems operated at or on behalf of the test facility
- Documentation of test facility
- Preparation and regular update of non-clinical studies related documents, site master plan, study plan, study report, SOPs, qualification master plan etc.
- The application of the GLP principles to non-clinical studies
- Inspections to determine if all studies are conducted in compliance with Principles of Good Laboratory Practice
- Cleaning and decontamination of facilities and equipment and minimizing sources of contamination of test items and test systems
- Ensuring that specialized equipment is properly used and maintained
- Ensuring proper conditions for test items and test systems etc.
Accredited medical and testing laboratories
- ČSN EN ISO/IEC 17025: 2018 standard for testing laboratories (since 2007)
- ČSN EN ISO 15189: 2013 standard for medical laboratories (since 2013)
- Areas of certified methods
- Analysis of alterations at the DNA and chromosomal level, in particular analysis of selected oncogenes and tumor suppressor genes, or their methylation status, using real-time PCR or next-generation sequencing (NGS)
- Examination of predictive and prognostic tumor markers in patients who are indicated for targeted therapy
- Analysis of RNA for the detection of circulating tumor cells in the most common solid tumors
- Analysis of DNA gene copy number changes in patients of various disease types using microarrays
- Analysis of tumor genes as treatment predictors using fluorescence in situ hybridization (FISH, CGH)
- Histochemical and immunohistochemical analysis of tissues, biopsies and cell lines
- Flow cytometry, especially cell ploidy and cell cycle analysis, determination of surface and intracellular antigens by immunofluorescence methods
- Cell subpopulations FACS sorting for further genomic and proteomic analyses