Section: 
General questions of otolaryngology
General questions of otolaryngologyIssues of integrating medical bioinformatics technologies into otorhinolaryngology: challenges and software solutions
A. A. Korneenkov (1), Yu. K. Yanov (2), E. E. Vyazemskaya (3), A. Yu. Medvedeva (4)
(1) Saint Petersburg Research Institute of Ear, Throat, Nose and Speech, Saint Petersburg, 190013, Russin Federation, (2) Kirov Military Medical Academy, Saint Petersburg, 194044, Russian Federation
UDK: УДК 575.112:004.43:616.21
DOI: https://doi.org/10.18692/1810-4800-2024-6-8-19
ABSTRACT
Abstract. Objective. To justify and propose a reproducible computing environment for implementing typical tasks of working with genetic sequences and the results of their analysis in scientific research and clinical practice based on the analysis of the prospects for the development of bioinformatics and omics technologies. Materials and methods. The study used data from literary sources, descriptions of known technologies for working with genetic sequences, educational materials from authoritative global educational organizations as well as our own experience in implementing reproducible research in scientific activities and medical education. The analysis of literary sources indicates that although otolaryngology is not the main focus of research on genotypic associations and the implementation of personalized (precision) medicine technologies, there is an objective need for these studies and technologies. The implementation of these needs is limited by an objective lack of relevant competencies of medical specialists in the field of informatics and biomedical statistics, the inability to master new, constantly developing omics technologies in the context of limited time resources as well as high requirements for computing power. In addition, in some cases, the low statistical reliability of genotypic associations is of significant importance for the prevalence of these technologies in clinical practice, which is expected to become acceptable as the volume and scale of studies increase. Results. The study proposes a model that reproduces the main elements and functions of working with genetic information, an integrated software environment and the content of typical computational tasks are proposed: from simple operations with genetic sequences of DNA, RNA, and amino acids to clinical interpretation of variants of an individual’s genetic sequences. An educational model of the process by which solutions to typical problems or «recipes» for processing genetic data are consistently studied is proposed. It uses a single terminology and data. To implement this model in otolaryngology, the R software environment and the Bioconductor project, which provides many separate packages for research in the field of bioinformatics, are proposed. It includes a set of tools for analyzing and understanding genomic data, annotations of biological sequences as well as the experimental data itself. During the study, a training package «mbioinf» was developed, containing materials and typical solutions for operations with genetic sequences in the R environment: creation of R-objects of genetic sequences, statistical analysis; paired and multiple alignment; search for motifs and patterns; working with resources of genetic annotations; detection of variants of genetic sequences, forecast of the influence of variants on amino acid sequences, and their clinical interpretation. The knowledge and skills obtained with the help of these recipes provide an understanding of the causes and consequences of variation in genetic sequences, identification of genotypic associations in ENT diseases and their practical application in the creation of informative diagnostic technologies.
Publication date:
17.12.2024
Keywords:
genotypic associations, bioinformatics, R program, Bioconductor, bioinformatics pipeline For citation:
Korneenkov A. A., Yanov Yu. K., Vyazemskaya E. E., Medvedeva A. Yu. Issues of integrating medical bioinformatics technologies into otorhinolaryngology: challenges and software solutions. Russian Otorhinolaryngology. 2024;23(6):8-19. (In Russ.) https://doi.org/10.18692/1810-4800-2024-6-8-19