The focus on precision medicine is a natural extension of the above-mentioned ELIXIR CZ expertise/strategic areas to medicine. As it is primarily genomics-driven, there is a very close connection with the genomics area, as well as with structural and chemical biology via drugs used for treatment. And, of course, there is a specific need for data access and management. The implementation of precision medicine approaches is almost always complex and disease specific. Resources are often fragmented and inherently very specific with respect to the kind of disease. Complex solutions are rare.
Human genomics plays an important role in this part, so it is necessary to consider the 1+MG (1+ Million Genomes) Initiative and B1MG (Beyond 1 Million Genomes) project. ELIXIR CZ is currently not the main driver of these activities in the Czech Republic. An evaluation of its deeper involvement can be done after a detailed mapping of the current situation, because there has not yet been a detailed survey of precision medicine stakeholders, their specific involvement and their needs in the Czech Republic. So, ELIXIR is involved in bioinformatics solutions for precision medicine, substantiated by the strategic partnership of ELIXIR and GA4GH.
The currently identified key domain of ELIXIR CZ is the development of tools and databases for a clinically relevant support system with focus on:
- Haematological/oncological malignancies. The processing of personal/biometric data, immunophenotyping, transcriptomic and genomic data (RNA-seq, single-cell RNA-seq, DNA-seq) – for the analysis of mechanisms of tumours relapse (chemoresistance, immune surveillance), protein mutation involved in cancer development and analysis of the binding process of an FDA/EMAapproved drug to said target proteins, the effect of mutations on protein function, for the detection of pathological mutations on mtDNA molecules, donor choice for hematopoietic stem cell transplantation (HSCT) and real-time interactive data exploration and reporting.
- Autoimmune and neurodegenerative diseases. Registry development for setting up tailor-made standardized multidisciplinary healthcare with validated clinical data for rare disease Amyotrophic lateral sclerosis (ALS), the detection of pathological mutations on mtDNA molecules with respect to neurodegenerative diseases, and the study of endogenous retroviruses and their association with diseases of the immune system.
ELIXIR CZ plans to implement a similar strategy to the most prominent ELIXIR members. To directly assist medical professionals as an infrastructure with the necessary complex solutions for using a precision medicine approach in their specific medical field, important steps need to be taken. So, the main challenge is a detailed mapping of the current situation, assessment of stakeholders’ needs, implementation of standards and the creation of logistical support in defined medical fields with a special focus on the Czech environment. As for the Federated EGA, ELIXIR CZ wants to focus on supporting those Czech stakeholders that generate data by providing them with sufficient knowledge and facilities, including tools for the subsequent handling and processing of this data for practical use. This action is closely related to the 1+MG activities.
Challenges and goals of ELIXIR CZ
- Goal 1: Mapping the current situation in the Czech Republic (state of the art, resources/tools used, national/international cooperation, infrastructure and project involvement, …) including possible ELIXIR CZ activities in 1+MG
Subsequently, depending on the results of Goal 1, the following goals will be pursued in specific medical fields:
- Goal 2: Setting up a strategy for the efficient and legally correct use and sharing of patient/individual health data
- Goal 3: Development in ELIXIR CZ identified key domains
- Improving and adapting existing tools for the specific needs of precision medicine
- Developing targeted computational and clinical decision support tools and services for diagnosis and therapy
- Participating in the creation of standardized databases with validated clinical data
- Goal 4: Establishing and strengthening the interaction between ELIXIR nodes and national infrastructures cooperating internationally, with a specific emphasis on defined Rare diseases
- Goal 5: Targeting the deployment of R&D tools into clinical practice and possibly industry