A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm
Fil: Fresno, Cristóbal. Universidad Católica de Córdoba; Argentina.
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| Formato: | publishedVersion article |
| Lenguaje: | Inglés |
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2024
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| Acceso en línea: | http://hdl.handle.net/11086/554521 https://doi.org/10.1093/bioinformatics/btw704 |
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I10-R141-11086-554521 |
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dspace |
| institution |
Universidad Nacional de Córdoba |
| institution_str |
I-10 |
| repository_str |
R-141 |
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Repositorio Digital Universitario (UNC) |
| language |
Inglés |
| topic |
Classification Rejection option PAM50 Molecular marker Breast cancer |
| spellingShingle |
Classification Rejection option PAM50 Molecular marker Breast cancer Fresno, Cristóbal González, Germán Alexis Merino, Gabriela Alejandra Flesia, Ana Georgina Podhajcer, Osvaldo Luis Llera, Andrea Sabina Fernández, Elmer Andrés A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| topic_facet |
Classification Rejection option PAM50 Molecular marker Breast cancer |
| description |
Fil: Fresno, Cristóbal. Universidad Católica de Córdoba; Argentina. |
| author2 |
https://orcid.org/0000-0001-9030-5622 |
| author_facet |
https://orcid.org/0000-0001-9030-5622 Fresno, Cristóbal González, Germán Alexis Merino, Gabriela Alejandra Flesia, Ana Georgina Podhajcer, Osvaldo Luis Llera, Andrea Sabina Fernández, Elmer Andrés |
| format |
publishedVersion article |
| author |
Fresno, Cristóbal González, Germán Alexis Merino, Gabriela Alejandra Flesia, Ana Georgina Podhajcer, Osvaldo Luis Llera, Andrea Sabina Fernández, Elmer Andrés |
| author_sort |
Fresno, Cristóbal |
| title |
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| title_short |
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| title_full |
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| title_fullStr |
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| title_full_unstemmed |
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm |
| title_sort |
novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on pam50 algorithm |
| publishDate |
2024 |
| url |
http://hdl.handle.net/11086/554521 https://doi.org/10.1093/bioinformatics/btw704 |
| work_keys_str_mv |
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I10-R141-11086-5545212024-12-11T06:38:14Z A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm Fresno, Cristóbal González, Germán Alexis Merino, Gabriela Alejandra Flesia, Ana Georgina Podhajcer, Osvaldo Luis Llera, Andrea Sabina Fernández, Elmer Andrés https://orcid.org/0000-0001-9030-5622 https://orcid.org/0000-0002-0130-6226 https://orcid.org/0000-0001-6936-3764 https://orcid.org/0000-0002-6512-8553 https://orcid.org/0000-0002-0089-0061 https://orcid.org/0000-0002-4711-8634 Classification Rejection option PAM50 Molecular marker Breast cancer info:eu-repo/semantics/publishedVersion Fil: Fresno, Cristóbal. Universidad Católica de Córdoba; Argentina. Fil: Fresno, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: González, Germán Alexis. Universidad Católica de Córdoba; Argentina. Fil: González, Germán Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Merino, Gabriela Alejandra. Universidad Católica de Córdoba; Argentina. Fil: Merino, Gabriela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Flesia, Ana Georgina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía, Física y Computación; Argentina. Fil: Flesia, Ana Georgina. Universidad Nacional de Córdoba. Centro de Investigación y Estudios de Matemática; Argentina. Fil: Flesia, Ana Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigación y Estudios de Matemática; Argentina. Fil: Podhajcer, Osvaldo Luis. Instituto Leloir. Laboratorio de Terapia Molecular y Celular; Argentina. Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Llera, Andrea Sabina. Instituto Leloir. Laboratorio de Terapia Molecular y Celular; Argentina. Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Fernández, Elmer Andrés. Universidad Católica de Córdoba; Argentina. Fil: Fernández, Elmer Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Motivation: The PAM50 classifier is used to assign patients to the highest correlated breast cancer subtype irrespectively of the obtained value. Nonetheless, all subtype correlations are required to build the risk of recurrence (ROR) score, currently used in therapeutic decisions. Present subtype uncertainty estimations are not accurate, seldom considered or require a population-based approach for this context. Results: Here we present a novel single-subject non-parametric uncertainty estimation based on PAM50’s gene label permutations. Simulations results (n= 5228) showed that only 61% subjects can be reliably "Assigned" to the PAM50 subtype, whereas 33% should be "Not Assigned" (NA), leaving the rest to tight "Ambiguous" correlations between subtypes. The NA subjects exclusion from the analysis improved survival subtype curves discrimination yielding a higher proportion of low and high ROR values. Conversely, all NA subjects showed similar survival behaviour regardless of the original PAM50 assignment. We propose to incorporate our PAM50 uncertainty estimation to support therapeutic decisions. info:eu-repo/semantics/publishedVersion Fil: Fresno, Cristóbal. Universidad Católica de Córdoba; Argentina. Fil: Fresno, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: González, Germán Alexis. Universidad Católica de Córdoba; Argentina. Fil: González, Germán Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Merino, Gabriela Alejandra. Universidad Católica de Córdoba; Argentina. Fil: Merino, Gabriela Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Flesia, Ana Georgina. Universidad Nacional de Córdoba. Facultad de Matemática, Astronomía, Física y Computación; Argentina. Fil: Flesia, Ana Georgina. Universidad Nacional de Córdoba. Centro de Investigación y Estudios de Matemática; Argentina. Fil: Flesia, Ana Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigación y Estudios de Matemática; Argentina. Fil: Podhajcer, Osvaldo Luis. Instituto Leloir. Laboratorio de Terapia Molecular y Celular; Argentina. Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Llera, Andrea Sabina. Instituto Leloir. Laboratorio de Terapia Molecular y Celular; Argentina. Fil: Llera, Andrea Sabina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Fernández, Elmer Andrés. Universidad Católica de Córdoba; Argentina. Fil: Fernández, Elmer Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Ciencias de la Información y Bioinformática (desarrollo de hardware va en 2.2 "Ingeniería Eléctrica, Electrónica y de Información" y los aspectos sociales van en 5.8 "Comunicación y Medios") 2024-12-10T14:09:17Z 2024-12-10T14:09:17Z 2017 article Fresno, C., González, G. A., Merino, G. A., Flesia, A. G., Podhajcer, O. L., Llera, A. S. y Fernández, E. A. (2017). A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures : its application on PAM50 algorithm. Bioinformatics, 33 (5), 693-700. https://doi.org/10.1093/bioinformatics/btw704 1367-4803 http://hdl.handle.net/11086/554521 1367-4811 https://doi.org/10.1093/bioinformatics/btw704 eng Atribución/Reconocimiento-NoComercial-SinDerivados 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/deed.es Impreso; Electrónico y/o Digital |