AP23483529: Software development and testing of targeting panels in nanopore gene sequencing for precision medicine

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

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.
Objectives: To develop software for the design and optimization of compatible primer sets for long distance multiplex PCR for the target genes. To develop a platform for comprehensive analysis of third generation amplicon sequencing data and analysis of identified variants. Investigate and evaluate the genotyping of mutations in the BRCA1/2, KRAS, NRAS, BRAF, PIK3CA and EGFR genes in tumour samples for the identification of rare variants using a gene panel for targeted third-generation sequencing analysis with ONT. To evaluate the genotyping of mutations in key biomarker genes in tumour samples for the identification of rare variants using targeted third-generation sequencing analysis. Mutational profiles will be identified and correlated with clinical outcomes (overall response rate; progression-free survival; overall survival).

The project will focus on the development of software for the design of gene panels using nanopore sequencing of the human genome that can be interpreted and applied by researchers and public health organizations. A diagnostic oncopanel will be developed as a precision assay based on targeted third-generation sequencing using Oxford Nanopore Technologies' genomic profiling solution to detect key biomarkers such as BRCA1/2, KRAS, NRAS, BRAF, PIK3CA and EGFR. A platform will be developed to comprehensively analyze amplicon sequencing data and analyze identified variants. A decision support tool will be used to match gene variants detected in the sequences with databases of known biomarkers, related therapies, clinical trials and guidelines. The results of this project will have important implications for medicine and public health. The research plan includes the publication of At least two (2) papers and/or reviews in peer-reviewed scientific publications that are in the 1st (first) and/or 2nd (second) quartile for impact factor in the Web of Science database and/or have a Scopus CiteScore percentile of at least seventy (70) in the Scopus database; or at least 1 (one) article or review in a peer-reviewed scientific publication indexed in the Science Citation Index Expanded and ranked in the 1st (first) quartile in the Web of Science database or have a Scopus CiteScore percentile of at least 90 (ninety) in the Scopus database.