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http://hdl.handle.net/2445/178832
Title: | Predicting MHC I restricted T cell epitopes in mice with NAP-CNB, a novel online tool |
Author: | Wert Carvajal, Carlos Sánchez García, Rubén Macías, José R Sanz Pamplona, Rebeca Méndez Pérez, Almudena Alemany Bonastre, Ramon Veiga, Esteban Sorzano, Carlos Óscar S. Muñoz Barrutia, Arrate |
Keywords: | Càncer Immunoteràpia Cèl·lules T Cancer Immunotherapy T cells |
Issue Date: | 24-May-2021 |
Publisher: | Springer Science and Business Media LLC |
Abstract: | Lack of a dedicated integrated pipeline for neoantigen discovery in mice hinders cancer immunotherapy research. Novel sequential approaches through recurrent neural networks can improve the accuracy of T-cell epitope binding affinity predictions in mice, and a simplified variant selection process can reduce operational requirements. We have developed a web server tool (NAP-CNB) for a full and automatic pipeline based on recurrent neural networks, to predict putative neoantigens from tumoral RNA sequencing reads. The developed software can estimate H-2 peptide ligands, with an AUC comparable or superior to state-of-the-art methods, directly from tumor samples. As a proof-of-concept, we used the B16 melanoma model to test the system's predictive capabilities, and we report its putative neoantigens. NAP-CNB web server is freely available at http://biocomp.cnb.csic.es/NeoantigensApp/ with scripts and datasets accessible through the download section. |
Note: | Reproducció del document publicat a: https://doi.org/10.1038/s41598-021-89927-5 |
It is part of: | Scientific Reports, 2021, vol. 11, num. 10780 |
URI: | http://hdl.handle.net/2445/178832 |
Related resource: | https://doi.org/10.1038/s41598-021-89927-5 |
Appears in Collections: | Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL)) |
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