Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
Thesis
Colorectal cancer (CRC) is the third most common cancer worldwide, with high mortality rates reported annually. While next-generation sequencing (NGS) has facilitated the characterization of mutational genomic profiles in several populations, our understanding of Colombian patients with CRC is limited. The aim of this research is to identify germline variants associated with CRC in this population, using a panel of 206 genes that includes clinically diagnostic panel genes and candidate genes obtained from literature studies. The methodology included two classification approaches: one based on ACMG/AMP (American College of Medical Genetics and Genomics and the Association for Molecular Pathology) recommendations to identify pathogenic and likely pathogenic variants (P/LP), and the other one using an artificial intelligence model called BoostDM. The results revealed significant rates of pathogenic variants, with 12% of patients having P/PP variants and 65% with oncodriver variants identified through BoostDM. These findings suggest the importance of using an extended panel for germline variant detection and considering the adoption of new variant classification strategies. Within the P/LP variants, three intronic variants located at splicing sites in candidate genes were identified. Functional validation of these variants using a minigene assay demonstrated the generation of aberrant transcripts attributed to splicing alterations. In conclusion, this study provided valuable insights into the prevalence and frequency of pathogenic variants in Colombian patients with CRC through NGS, using two different classification approaches. Additionally, the functional effect of three intronic variants was successfully tested, supporting the hypothesis of protein-level damage induced by these variants. Overall, this study contributes to the genomic knowledge of unselected CRC patients in the Colombian population, producing new perspectives for the clinical and translational application aimed at early identification and the implementation of strategies to improve the prognosis and survival of carriers of pathogenic variants. To our knowledge, this study represents the first approach in the country to address this strategy in unselected CCR patients.
