Software development and testing of targeting panels in nanopore gene sequencing for precision medicine
2025-05-15 15:37
Project goal: The aim of the project is to develop and test software for the design of targeted gene panels for long fragment sequencing using nanopore technology.
Project description: 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).
PI: Ruslan Kalendar
Expected results: 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.
Methodology: We will use the available "National Laboratory Astana" collection of specimen and data of full genome sequencing of patients and healthy individuals recruited in the Republic of Kazakhstan. Amplicon sequencing using Oxford Nanopore Technologies (ONT). Bioinformatics methods using machine learning and molecular biology techniques.