Software development and testing of targeting panels in nanopore gene sequencing for precision medicine

Cancer is generally recognized as a genomic disease caused by genetic alterations in different classes of genes that disrupt essential cellular processes that control cell development and differentiation. These classes include tumour suppressor genes, which protect cells from cancer, and oncogenes, which control cell differentiation and replication but can facilitate cancer progression if they become mutated. As gene mutations accumulate, they simultaneously deactivate cell-protective processes and overactivated cell replication and differentiation. Next-generation sequencing (NGS) is being implemented in clinical laboratories worldwide to identify genomic variants in cancer and ultimately improve patient outcomes. Massively sequencing the entire genome, or exome, of tumour cells has been instrumental in elucidating complex biological questions. The amount of data generated by these techniques is challenging to manage in a clinical context, making them currently impractical for widespread use. Instead, the dominant strategy is to perform targeted sequencing on a subset of genes of clinical relevance. This approach offers the best compromise between precise identification of genomic alterations, high sensitivity and a favorable cost-benefit ratio. The data derived from targeted DNA sequencing can aid in diagnostic categorization, direct therapeutic solutions and provide predictive outlooks. The use of condensed gene panels streamlines sample handling while simplifying data analysis, interpretation of results and medical reporting, ultimately impacting patient care. The choice of sequencing method and panel size for routine testing should consider diagnostic yield, clinical utility, sample availability and turnaround time as critical factors.
The aim of the project is to develop and test software for the design of targeted gene panels for nanopore technology sequencing.

Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan