Scientists, Doctors, and Informaticians in Brno Develop Unique Bioinformatics Software
3. June 2020
Bioinformaticians from the Brno-based life science research centre, CEITEC Masaryk University, succeeded in the fourth public call of TACR ZETA, which supports applied research. A multidisciplinary team of scientists led by bioinformatician Vojtech Bystry, is currently developing a novel computer application for clinical use that will enable the integration of genomic and transcriptomic data obtained by next generation sequencing. A team of experts consisting of informaticians, geneticists, molecular biologists, oncologists, and haematologists are working together on this unique clinical research project. Scientists from CEITEC MU, software developers from the private Brno company, Apps Dev Team, and doctors from the Department of Paediatric Oncology at the University Hospital Brno (FN Brno) aim to improve the diagnosis of at-risk paediatric patients with solid tumours. The involved experts are using the newest bioinformatics tools to unify several scientific procedures into a predictive model that is embedded into a high-quality software framework. This novel bioinformatic tool will be developed within the next two years and will serve doctors as a more sophisticated treatment planning tool for paediatric oncology patients.
Next-generation sequencing (NGS) is a term used to describe a number of various modern DNA sequencing technologies that identify nucleotide sequences contained in DNA. These technologies are used in many research fields and enable DNA and RNA sequencing to become much faster and cheaper than the previously used Sanger sequencing. NGS has revolutionised the study of genomics and molecular biology allowing researchers to study biological systems at an unprecedent level. Using NGS, scientists are able to analyse the entire human genome in a single sequencing experiment or study epigenetic factors. Czech scientists are not lagging behind their foreign colleagues in the usage of this technology. The research group of Professor Ondrej Slaby from CEITEC MU has been collaborating with doctors from the Department of Pediatric Oncology at the Brno University Hospital on a long-term project focused on precision oncology in high-risk paediatrics patients. The scientists have determined the detailed characteristic of the tumor molecular structure using the most modern investigative techniques. For each molecular analysis of the tumour, researchers perform up to four different NGS analyses and prepare a detailed clinical report. This report is used by a panel of experts as a basis when deciding on the next therapeutic procedure of a particular patient. The most recently published research confirms that each of these analyses represents further improvement in the accurate classification of certain types of tumours.
Data analysis of individual next-generation sequencing tests typically requires the use of a specifically designed computational pipeline. Commercially available NGS data analysis tools exist, but none of these tools have the ability to combine multiple NGS analyses into a single result. "Based on the available sources of information, we know that there are currently no universal bioinformatics solutions available that allow for the combination of several different types of analyses to comprehensively evaluate the data of a single patient. Therefore, we decided to develop such an application ourselves. We are aiming for a high-quality solution that will enable a comprehensive analysis of complex sequencing data sets and that will accelerate and refine the complex evaluation process. Our tool could also simplify the transfer of the newest scientific knowledge from molecular medicine into clinical practice," explained Vojtech Bystry, project investigator of this topic.
This software application will be able to consolidate all NGS data for the purpose of diagnosis and clinical characteristics of oncological patients and to integrate the results of multiple NGS examinations for each patient. The integration of results will be carried out on the basis of a clinical association model designed by an expert clinical geneticist. The proposed application will be able to control the NGS examination process, from sample registration to automatic bioinformatics processing, to the visualisation of results. The application will be designed using modern software development techniques that emphasise reliability and long-term sustainable development. The Austrian Medical University of Vienna has already expressed interest in this application that is currently under development.
Brno as a Mecca of Science and Information Technology
The main mentor of the project is the head of the Bioinformatics Core Facility at CEITEC MU, Panagiotis Alexiou, who joined CEITEC MU more than two years ago from the University of Pennsylvania in the United States. A huge added value of this project is the cooperation between experts from the academic and private sectors, and their extensive expertise in the fields of software development, bioinformatics, and molecular medicine. The partnering company, Apps Dev Team, is a young, dynamically expanding IT company that already has extensive experience in developing high-quality commercial information systems, such as the well-known IDOS app for public transport connections. The team of developers from Brno will have a unique opportunity to work with the latest technologies in the field of molecular medicine and to participate in clinical research activities that have a very rich social benefit.
"We hope that the development of a concrete product with visible social impact will increase the interest of young talent in science and information technology. I also hope that we will inspire other academic actors to connect with the private sector, as this is something in which we see huge untapped potential, especially in our region," added Jiri Nantl, Director of CEITEC Masaryk University. All of the scientists involved will have the opportunity to participate in the development of this bioinformatics application with an experienced private company, using the latest technologies and processes of software development. Scientists will have a chance to adopt an agile approach to project management and other modern software development methodologies.
Within two years, this new unique application should be able to serve doctors at the Clinic of Paediatric Oncology at the Brno University Hospital and their high-risk paediatric patients that have solid tumours. This software solution will accelerate, simplify, and refine data analysis, thereby also reducing the likelihood of an error in the diagnosis process and evaluation. In addition, the solution will simplify, and thus accelerate, the introduction of the latest scientific knowledge into the diagnostic process. This will improve patient stratification, which will have a positive effect on better treatment settings and the health of paediatric patients. "It is a reasonable assumption that over the next five to ten years, NGS technology will become more affordable and routinely available to the mainstream health sector, resulting in a massive commercial potential of our application. Companies with experience and expertise in this emerging multidisciplinary field will have a competitive advantage," added Panagiotis Alexiou.
Author: Ester Jarour
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