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Artículo
Autoencoded DNA methylation data to predict breast cancer recurrence: Machine learning models and gene-weight significance
Autor/es | Macías García, Laura
Martínez Ballesteros, María del Mar Luna Romera, José María García Heredia, José Manuel García Gutiérrez, Jorge Riquelme Santos, José Cristóbal |
Departamento | Universidad de Sevilla. Departamento de Lenguajes y Sistemas Informáticos Universidad de Sevilla. Departamento de Citología e Histología Normal y Patológica Universidad de Sevilla. Departamento de Bioquímica Vegetal y Biología Molecular |
Fecha de publicación | 2020 |
Fecha de depósito | 2022-04-12 |
Publicado en |
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Resumen | Breast cancer is the most frequent cancer in women and the second most frequent overall after lung cancer.
Although the 5-year survival rate of breast cancer is relatively high, recurrence is also common which often ... Breast cancer is the most frequent cancer in women and the second most frequent overall after lung cancer. Although the 5-year survival rate of breast cancer is relatively high, recurrence is also common which often involves metastasis with its consequent threat for patients. DNA methylation-derived databases have become an interesting primary source for supervised knowledge extraction regarding breast cancer. Unfortunately, the study of DNA methylation involves the processing of hundreds of thousands of features for every patient. DNA methylation is featured by High Dimension Low Sample Size which has shown well-known issues regarding feature selection and generation. Autoencoders (AEs) appear as a specific technique for conducting nonlinear feature fusion. Our main objective in this work is to design a procedure to summarize DNA methylation by taking advantage of AEs. Our proposal is able to generate new features from the values of CpG sites of patients with and without recurrence. Then, a limited set of relevant genes to characterize breast cancer recurrence is proposed by the application of survival analysis and a pondered ranking of genes according to the distribution of their CpG sites. To test our proposal we have selected a dataset from The Cancer Genome Atlas data portal and an AE with a single-hidden layer. The literature and enrichment analysis (based on genomic context and functional annota tion) conducted regarding the genes obtained with our experiment confirmed that all of these genes were related to breast cancer recurrence. |
Agencias financiadoras | Ministerio de Economía y Competitividad (MINECO). España |
Identificador del proyecto | TIN2014-55894-C2-R
TIN2017-88209-C2-2-R |
Cita | Macías García, L., Martínez Ballesteros, M.d.M., Luna Romera, J.M., García Heredia, J.M., García Gutiérrez, J. y Riquelme Santos, J.C. (2020). Autoencoded DNA methylation data to predict breast cancer recurrence: Machine learning models and gene-weight significance. Artificial Intelligence in Medicine, 110 (November 2020, art. nº101976) |
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