Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana

El cáncer colorrectal (CCR) es el tercer tipo de cáncer de mayor incidencia a nivel mundial, con altas tasas de mortalidad reportadas anualmente. A pesar de que la secuenciación de próxima generación (NGS) ha permitido caracterizar perfiles genómicos mutacionales en diversas poblaciones, la informac...

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Fecha de publicación:: 2023

Institución:: Universidad del Rosario

Repositorio:: Repositorio EdocUR - U. Rosario

Idioma:: spa

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network_acronym_str	EDOCUR2
network_name_str	Repositorio EdocUR - U. Rosario
repository_id_str
dc.title.none.fl_str_mv	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
dc.title.TranslatedTitle.none.fl_str_mv	Functional genomics for the description of germline mutations in the molecular diagnosis of unselected colorectal cancer in the Colombian population
title	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
spellingShingle	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana Cáncer colorrectal Secuenciación de próxima generación (NGS) Variantes germinales patogénicas Inteligencia artificial Minigenes Validación funcional Pathogenic germline variants Next Generation sequencing (NGS) Artificial intelligence Minigenes Functional validation Colorectal cancer
title_short	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
title_full	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
title_fullStr	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
title_full_unstemmed	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
title_sort	Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana
dc.contributor.advisor.none.fl_str_mv	Fonseca Mendoza, Dora Janeth Morel, Adrien
dc.subject.none.fl_str_mv	Cáncer colorrectal Secuenciación de próxima generación (NGS) Variantes germinales patogénicas Inteligencia artificial Minigenes Validación funcional
topic	Cáncer colorrectal Secuenciación de próxima generación (NGS) Variantes germinales patogénicas Inteligencia artificial Minigenes Validación funcional Pathogenic germline variants Next Generation sequencing (NGS) Artificial intelligence Minigenes Functional validation Colorectal cancer
dc.subject.keyword.none.fl_str_mv	Pathogenic germline variants Next Generation sequencing (NGS) Artificial intelligence Minigenes Functional validation Colorectal cancer
description	El cáncer colorrectal (CCR) es el tercer tipo de cáncer de mayor incidencia a nivel mundial, con altas tasas de mortalidad reportadas anualmente. A pesar de que la secuenciación de próxima generación (NGS) ha permitido caracterizar perfiles genómicos mutacionales en diversas poblaciones, la información específica sobre pacientes colombianos con CCR es limitada. El objetivo de esta investigación es identificar variantes germinales asociadas al CCR en dicha población, utilizando un panel de 206 genes que incluye tanto genes de paneles de diagnóstico clínico como genes candidatos obtenidos de estudios de literatura. La metodología empleada incluyó dos enfoques de clasificación: uno basado en las recomendaciones de la ACMG/AMP (American College of Medical Genetics and Genomics and the Association for Molecular Pathology) para identificar variantes patogénicas y probablemente patogénicas (P/PP), y otro utilizando el modelo de inteligencia artificial BoostDM. Los resultados obtenidos revelaron tasas significativas de variantes patogénicas, con un 12% de pacientes con variantes P/PP y un 65% con variantes “oncodriver” identificadas mediante BoostDM. Estos hallazgos sugieren la importancia de utilizar un panel ampliado en la detección de variantes germinales y la consideración de adoptar e indagar en nuevas estrategias de clasificación de variantes. Entre las variantes P/PP, se identificaron tres variantes intrónicas en sitios de splicing en genes candidatos. La validación funcional de estas variantes mediante un ensayo de minigenes demostró la generación de transcritos aberrantes, debido a la alteración en el splicing. En conclusión, esta investigación proporcionó información valiosa sobre la presencia y frecuencia de variantes patogénicas en pacientes colombianos con CCR, usando un análisis genómico ampliado mediante NGS, utilizando dos enfoques bioinformáticos. Adicionalmente, se logró probar funcionalmente el efecto de tres variantes intrónicas de interés, que demostró la consecuencia molecular de estas y la potencial implicación a nivel de la proteína. En conjunto, este estudio contribuye al conocimiento del perfil genómico de pacientes no seleccionados con CCR en la población colombiana, generando nuevas perspectivas para la aplicación clínica y traslacional que busca la identificación temprana y la aplicación de estrategias que mejoren el pronóstico y supervivencia de los portadores de variantes de interés. Para nuestro conocimiento, esta corresponde a la primera aproximación en el país que aborda esta estrategia en pacientes no seleccionados con CCR.
publishDate	2023
dc.date.created.none.fl_str_mv	2023-12-01
dc.date.accessioned.none.fl_str_mv	2024-02-14T11:49:18Z
dc.date.available.none.fl_str_mv	2024-02-14T11:49:18Z
dc.date.embargoEnd.none.fl_str_mv	info:eu-repo/date/embargoEnd/2026-02-15
dc.type.none.fl_str_mv	bachelorThesis
dc.type.coar.fl_str_mv	http://purl.org/coar/resource_type/c_7a1f
dc.type.document.none.fl_str_mv	Trabajo de grado
dc.type.spa.none.fl_str_mv	Pre-print
dc.identifier.doi.none.fl_str_mv	https://doi.org/10.48713/10336_42238
dc.identifier.uri.none.fl_str_mv	https://repository.urosario.edu.co/handle/10336/42238
url	https://doi.org/10.48713/10336_42238 https://repository.urosario.edu.co/handle/10336/42238
dc.language.iso.none.fl_str_mv	spa
language	spa
dc.rights.*.fl_str_mv	Attribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.coar.fl_str_mv	http://purl.org/coar/access_right/c_f1cf
dc.rights.acceso.none.fl_str_mv	Restringido (Temporalmente bloqueado)
dc.rights.uri.*.fl_str_mv	http://creativecommons.org/licenses/by-nc-nd/4.0/
rights_invalid_str_mv	Attribution-NonCommercial-NoDerivatives 4.0 International Restringido (Temporalmente bloqueado) http://creativecommons.org/licenses/by-nc-nd/4.0/ http://purl.org/coar/access_right/c_f1cf
dc.format.extent.none.fl_str_mv	47 pp
dc.format.mimetype.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Universidad del Rosario
dc.publisher.department.none.fl_str_mv	Facultad de Ciencias Naturales
dc.publisher.program.none.fl_str_mv	Maestría en Ciencias Naturales
publisher.none.fl_str_mv	Universidad del Rosario
institution	Universidad del Rosario
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spelling	Fonseca Mendoza, Dora Janeth52094825600Morel, Adrien682778600Rodríguez Salamanca, Juliana ValentinaMagíster en Ciencias NaturalesMaestríaFull timec094bb96-032b-44ef-ae57-a2291ac49ea02024-02-14T11:49:18Z2024-02-14T11:49:18Z2023-12-01info:eu-repo/date/embargoEnd/2026-02-15El cáncer colorrectal (CCR) es el tercer tipo de cáncer de mayor incidencia a nivel mundial, con altas tasas de mortalidad reportadas anualmente. A pesar de que la secuenciación de próxima generación (NGS) ha permitido caracterizar perfiles genómicos mutacionales en diversas poblaciones, la información específica sobre pacientes colombianos con CCR es limitada. El objetivo de esta investigación es identificar variantes germinales asociadas al CCR en dicha población, utilizando un panel de 206 genes que incluye tanto genes de paneles de diagnóstico clínico como genes candidatos obtenidos de estudios de literatura. La metodología empleada incluyó dos enfoques de clasificación: uno basado en las recomendaciones de la ACMG/AMP (American College of Medical Genetics and Genomics and the Association for Molecular Pathology) para identificar variantes patogénicas y probablemente patogénicas (P/PP), y otro utilizando el modelo de inteligencia artificial BoostDM. Los resultados obtenidos revelaron tasas significativas de variantes patogénicas, con un 12% de pacientes con variantes P/PP y un 65% con variantes “oncodriver” identificadas mediante BoostDM. Estos hallazgos sugieren la importancia de utilizar un panel ampliado en la detección de variantes germinales y la consideración de adoptar e indagar en nuevas estrategias de clasificación de variantes. Entre las variantes P/PP, se identificaron tres variantes intrónicas en sitios de splicing en genes candidatos. La validación funcional de estas variantes mediante un ensayo de minigenes demostró la generación de transcritos aberrantes, debido a la alteración en el splicing. En conclusión, esta investigación proporcionó información valiosa sobre la presencia y frecuencia de variantes patogénicas en pacientes colombianos con CCR, usando un análisis genómico ampliado mediante NGS, utilizando dos enfoques bioinformáticos. Adicionalmente, se logró probar funcionalmente el efecto de tres variantes intrónicas de interés, que demostró la consecuencia molecular de estas y la potencial implicación a nivel de la proteína. En conjunto, este estudio contribuye al conocimiento del perfil genómico de pacientes no seleccionados con CCR en la población colombiana, generando nuevas perspectivas para la aplicación clínica y traslacional que busca la identificación temprana y la aplicación de estrategias que mejoren el pronóstico y supervivencia de los portadores de variantes de interés. Para nuestro conocimiento, esta corresponde a la primera aproximación en el país que aborda esta estrategia en pacientes no seleccionados con CCR.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.Hospital Universitario Mayor MéderiUniversidad del Rosario47 ppapplication/pdfhttps://doi.org/10.48713/10336_42238https://repository.urosario.edu.co/handle/10336/42238spaUniversidad del RosarioFacultad de Ciencias NaturalesMaestría en Ciencias NaturalesAttribution-NonCommercial-NoDerivatives 4.0 InternationalRestringido (Temporalmente bloqueado)http://creativecommons.org/licenses/by-nc-nd/4.0/http://purl.org/coar/access_right/c_f1cf (2022) Cuenta de alto costo (CAC) /HIGIA. Disponible en: https://cuentadealtocosto.org/higia/cancer-morbimortalidad-demografico/. Ahmad, Rehan; Singh, Jaikee kumar; Wunnava, Amoolya; Al-obeed, Omar; Absulla, Maha; Srivastava, Sandeep Kumar (2021) Emerging trends in colorectal cancer: Dysregulated signaling pathways (Review). 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Genómica funcional para la descripción de mutaciones germinales en el diagnóstico molecular del cáncer de colon y recto no seleccionado en población colombiana

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