About the Czech Centre for Phenogenomics
The Czech Centre for Phenogenomics is a large research infrastructure unique in combining genetic engineering capabilities, advanced phenotyping and imaging modalities, specific pathogen free (SPF) animal housing and husbandry, as well as cryopreservation and archiving, all in one central location – at BIOCEV campus. This concentration of specialized infrastructure and expertise provides a unique and valuable resource for the biomedical and biotechnology research community.
Genetically modified mouse models have become a key tool in basic and biomedical research. The ability to engineer the mouse genome has greatly transformed biomedical research in the last decade. Crucial for this technology is the ability to control the expression of genes of interest. It is possible to increase or decrease gene expression, or eliminate the expression of a gene completely. Transgenic and gene knockout/knockin technologies have become important experimental tools for assigning functions to genes at the level of whole complexity of organism, creating models of genetic disorders, evaluating effects drugs and toxins, thus helping to answer fundamental issues in basic and applied research.
The Czech Centre for Phenogenomics (CCP), through its membership in INFRAFRONTIER and IMPC, is a partner in a collective global network that aims to comprehensively and systematically analyze the effect of loss of function gene mutations in mice. The goal is to produce a comprehensive ‘encyclopedia‘ of gene function, that will help identify causative factors of human diseases as well as novel targets for therapeutic intervention. Through the adoption of standardized procedures and pipelines, and the usage of quality control measures and cross-validation, our shared goal is to produce high-quality data that will not only function as a scientific reference catalog, but will also enable comprehensive meta-analyses that could uncover otherwise hidden disease relationships and functional interactions. By focusing expertise and resources and coordinating our efforts to avoid redundant work, we will help achieve these goals in a more cost-effective manner.
The CCP has planned for its phenotyping capabilities to accommodate both mouse and rat disease models. Although the mouse remains the most cost-effective choice for comprehensive phenotyping, the rat remains a better model for a number of human conditions, including cardiovascular disease, diabetes and behavioral disorders. Through the generation and focused phenotyping of prospective rat models, where gene targets have been identified through the systematic mouse phenotyping effort, we focus our complementary analyses to conditions where the larger size and higher cognitive function of the rat is advantageous for more complex and accurate physiological assessments.
Organizational Structure
The governance of CCP is based on three principles: institutional anchoring within IMG, central strategic leadership by the CCP Director, and delegated operational responsibility to Module Heads. Within this framework, CCP is managed by the CCP Director (and Principal Investigator) as one coordinated infrastructure. CCP includes the following Modules: Management CCP, Transgenic and Archiving Module, Research Solutions and Strategy Module, Animal Facility component, Phenotyping Module, New Approach Methodologies Module, Models of Infectious Diseases Module, Preclinical Evaluation Module, and Data Science Module. These Modules are organised into four functional pillars. Module Heads are accountable not only for scientific quality and service delivery, but also for compliant, transparent, efficient, and well-coordinated operation of their respective modules within the integrated CCP infrastructure.
Central Management Module (CMM)
The Central Management Module provides executive and scientific leadership, business development, invention disclosure monitoring and initiation of intellectual-property actions, administrative coordination, and institutional representation. It serves as the main management backbone of CCP and supports the CCP Director in the overall governance of the infrastructure.
Research Solutions and Strategy Module (RSM)
RSM is the strategic hub for project design, grant solutions, RD-Factory activities and technology development. It is intentionally organised as a development and solution-design interface that translates funding opportunities and complex user demands into implementable workflows across the other CCP modules.
Transgenic and Archiving Module (TAM)
TAM is responsible for rodent model generation, genotyping, cryopreservation and distribution. It remains one of the core legacy modules and forms a major part of the model-generation capacity of CCP.
Animal Facility Module (AFM)
The animal facility module secures breeding, housing, animal welfare and import/export operations for the CCP animal platforms.
New Approach Methodologies Module (NAM)
NAM develops human cell-based and complementary non-animal models, including organoids and 2D/3D systems, together with standardised workflows for their characterisation. It extends CCP from a rodentfocused infrastructure toward an integrated in vivo and in vitro platform aligned with 3R principles and translational needs.
Phenotyping Module (PM)
PM provides standardised physiological and functional phenotyping across major biological systems and remains a key service engine of CCP. It is focused primarily on testing gene functions and detailed biological characterisation.
Models of Infectious Diseases Module (MID)
MID operates the BSL-3 platform and infection models and phenotyping workflows. It expands CCP’s role into high-containment infectious-disease research and forms a strategic component of CCP’s future role in ERINHA-CZ and related preparedness activities.
Preclinical Evaluation Module (PEM)
PEM concentrates activities related to therapeutic assessment, toxicology, pharmacology and GLPcompliant or GLP-like preclinical studies, and other activities supporting or close to in vivo phenotyping. Its establishment clearly separates therapy-oriented testing from the gene-function phenotyping mission of PM and strengthens CCP’s translational and contract-research capacity.
Digital Phenotyping / Data Science Module (DSM)
DSM integrates bioinformatics, computational biology, statistics, AI and machine learning, data infrastructure and digital phenotyping workflows. It converts distributed experimental outputs into robust, FAIR and reusable knowledge and serves all other CCP modules as a cross-cutting analytical platform. DSM is also responsible for Data Management Plan (DMP) of CCP.