Translation. Region: Russian Federation –
Source: Novosibirsk State University –
An important disclaimer is at the bottom of this article.
VarAn (variant, analyzer) software, designed for the comprehensive processing and analysis of genomic data obtained by high-throughput sequencing, was developed by researchers at the Bioinformatics Laboratory. Institute of Medicine and Medical Technologies (IMMT) of Novosibirsk State UniversityIn September of this year, the program received a state registration certificate, legally securing the copyright to the development and opening the door to its further commercialization and implementation in clinical practice. In the near future, the developers will submit to the Federal Service for Surveillance in Healthcare (Roszdravnadzor) a complete package of documents required to obtain a registration certificate for the medical device, which this application will serve as. The next stage of the project involves clinical trials of the developed solutions, using clinical samples and evaluating the system's diagnostic performance under real-world conditions.
— In recent years, with the active introduction of genetic testing in the diagnosis of hereditary and oncological diseases, the need for specialized software capable of coping with these tasks has increased significantly. Programs similar in functionality to our development exist in Russia and abroad, but the difference between our product is its ability to support a wider range of possible analyzes and evaluate both somatic and hereditary mutations, which expands the possibilities of its use and provides advantages for use in clinical practice. Our program analyzes DNA sequencing data. This process is the reading of a DNA sequence. This is important because many diseases – both hereditary and oncological – arise precisely because of the replacement of the DNA sequence. To prescribe specialized treatment, it is necessary to read the patient’s DNA sequence and determine which mutation caused the disease. Until recently, specialists could only read very short fragments of it, and not with the highest accuracy. And to obtain reliable information about an existing mutation, it is necessary to read many such sequences. The result is millions of short reads, and in order to identify the desired mutations in this array of information, it is necessary to perform complex computer processing of the available data. Our VarAn software performs all the stages of analyzing such short DNA reads: assessing their quality, filtering, and then mapping to the reference genome, determining the mutation and its annotation – does it affect the protein, is it responsible for the presence of any disease. As a result, the user receives a full report that lists all potentially significant clinical mutations,” explained VarAn software developer, junior researcher at the Bioinformatics Laboratory of the Institute of Medical Sciences of NSU Alexander Vikhorev.
VarAn software has a wide range of applications. It is designed for automated analysis of high-throughput sequencing (NGS) data in clinical practice to identify and interpret pathogenic genetic variants for diagnostic purposes. The program covers the full data processing cycle: from raw sequencing data quality control (FASTQ) to generating a clinical report containing annotated variants with established diagnostic significance.
"Our VarAn app is a standalone product with expanded functionality for clinical diagnostics. It offers versatility for a wide range of genetic studies and provides comprehensive bioinformatics analysis with automated interpretation of the clinical significance of identified variants. It integrates the full NGS data processing cycle into a single software environment. The output data is intended for use by medical professionals in making diagnostic decisions and developing personalized therapeutic strategies," explained Alexander Vikhorev.
The VarAn app features a user-friendly, intuitive interface for managing analysis results and provides a secure connection to ensure the confidentiality of medical data. Using it requires no specialized knowledge, let alone programming skills. The results display form is also extremely user-friendly.
"Our software is designed for a select group of professional users, primarily scientists and geneticists. For their convenience, the application has preset optimal parameters: simply upload sample data, initiate the analysis using a simple web form, select a few parameters—for example, the genome version—and run the process. Then, simply wait for the analysis to complete, which, depending on the data volume, can take anywhere from a few hours to several days. The results viewer is also extremely simple and user-friendly. Right on the application's website, you can view mutations, filter them, view the results in a genomic browser, and receive a detailed sequencing quality report. If necessary, you can download the results as an Excel spreadsheet for further independent work with them offline. Any physician can initiate the analysis using our website; no specialized programming knowledge or specialized applications are required," the developer explained.
The web application is hosted on the varan.nsu.ru domain, where technical testing of the system is currently underway using real genomic data. Laboratory staff are conducting these tests internally, without the involvement of external users. The reference genomes used in the tests have previously been sequenced and analyzed multiple times by specialists, who identified reference mutations in them. The website has successfully passed all operational modes, demonstrating the software's high sensitivity and specificity.
VarAn software was created as part of a project to develop comprehensive disease diagnostic solutions using whole-genome sequencing and microfluidic technologies. This project is part of the strategic technology project "Center for the Integration of Biomedicine and Pharmaceutics," implemented with the support of the Priority 2030 program.
Material prepared by: Elena Panfilo, NSU press service
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