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4. Machine Learning-Assisted Recurrence Prediction for Early-Stage Non-Small-Cell Lung Cancer Patients

Author

Janik, Adrianna, Torrente, Maria, Costabello, Luca, Calvo, Virginia, Walsh, Brian, Camps, Carlos, Mohamed, Sameh K., Ortega, Ana L., Nováček, Vít, Massutí, Bartomeu, Minervini, Pasquale, Campelo, M. Rosario Garcia, del Barco, Edel, Bosch-Barrera, Joaquim, Menasalvas, Ernestina, Timilsina, Mohan, and Provencio, Mariano

Subjects
Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods
Abstract

Background: Stratifying cancer patients according to risk of relapse can personalize their care. In this work, we provide an answer to the following research question: How to utilize machine learning to estimate probability of relapse in early-stage non-small-cell lung cancer patients? Methods: For predicting relapse in 1,387 early-stage (I-II), non-small-cell lung cancer (NSCLC) patients from the Spanish Lung Cancer Group data (65.7 average age, 24.8% females, 75.2% males) we train tabular and graph machine learning models. We generate automatic explanations for the predictions of such models. For models trained on tabular data, we adopt SHAP local explanations to gauge how each patient feature contributes to the predicted outcome. We explain graph machine learning predictions with an example-based method that highlights influential past patients. Results: Machine learning models trained on tabular data exhibit a 76% accuracy for the Random Forest model at predicting relapse evaluated with a 10-fold cross-validation (model was trained 10 times with different independent sets of patients in test, train and validation sets, the reported metrics are averaged over these 10 test sets). Graph machine learning reaches 68% accuracy over a 200-patient, held-out test set, calibrated on a held-out set of 100 patients. Conclusions: Our results show that machine learning models trained on tabular and graph data can enable objective, personalised and reproducible prediction of relapse and therefore, disease outcome in patients with early-stage NSCLC. With further prospective and multisite validation, and additional radiological and molecular data, this prognostic model could potentially serve as a predictive decision support tool for deciding the use of adjuvant treatments in early-stage lung cancer. Keywords: Non-Small-Cell Lung Cancer, Tumor Recurrence Prediction, Machine Learning

Published
2022

6. Perioperative chemotherapy and nivolumab in non-small-cell lung cancer (NADIM): 5-year clinical outcomes from a multicentre, single-arm, phase 2 trial

Author

Provencio, Mariano, Nadal, Ernest, Insa, Amelia, García Campelo, Rosario, Casal, Joaquín, Dómine, Manuel, Massuti, Bartomeu, Majem, Margarita, Rodríguez-Abreu, Delvys, Martínez-Martí, Alex, de Castro, Javier, Gómez de Antonio, David, Macia, Iván, Figueroa, Santiago, Fernández Vago, Luís, Calvo, Virginia, Palmero, Ramón, Sierra-Rodero, Belén, Martínez-Toledo, Cristina, Molina-Alejandre, Marta, Serna-Blasco, Roberto, Romero, Atocha, and Cruz-Bermúdez, Alberto

Published
2024
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9. Family history of cancer and lung cancer: Utility of big data and artificial intelligence for exploring the role of genetic risk

Author

Calvo, Virginia, Niazmand, Emetis, Carcereny, Enric, Rodriguez-Abreu, Delvys, Cobo, Manuel, López-Castro, Rafael, Guirado, María, Camps, Carlos, Laura Ortega, Ana, Bernabé, Reyes, Massutí, Bartomeu, Garcia-Campelo, Rosario, del Barco, Edel, Luis González-Larriba, José, Bosch-Barrera, Joaquim, Martínez, Marta, Torrente, María, Vidal, María-Esther, and Provencio, Mariano

Published
2024
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10. BRAF mutational status is associated with survival outcomes in locally advanced resectable and metastatic NSCLC

Author

Provencio, Mariano, Robado de Lope, Lucía, Serna-Blasco, Roberto, Nadal, Ernest, Diz Tain, Pilar, Massuti, Bartomeu, González-Larriba, José Luis, Insa, Amelia, Sánchez-Hernández, Alfredo, Casal-Rubio, Joaquín, García-Campelo, Rosario, Sequero López, Silvia, Rogado, Jacobo, Martínez-Martí, Alex, Bosch-Barrera, Joaquim, Bernabé, Reyes, Vázquez Estévez, Sergio, Ponce, Santiago, de Castro, Javier, Coves Sarto, Juan, Reguart, Noemí, Dómine, Manuel, Aguilar, Andrés, Majem, Margarita, Estival, Anna, Peña Cabia, Silvia, López Martín, Ana, Sala González, María Ángeles, Cobo, Manuel, Camps, Carlos, Barneto, Isidoro, Calvo, Virginia, Collazo-Lorduy, Ana, Cruz-Bermúdez, Alberto, and Romero, Atocha

Published
2024
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12. Describing differences among populations of thoracic tumors patients under and over 80 years: Data analysis from the SLCG thoracic tumor registry

Author

Provencio, Mariano, Cobo, Manuel, Rodriguez-Abreu, Delvys, Carcereny, Enric, Cantero, Alexandra, Calvo, Virginia, López Castro, Rafael, Bernabé, Reyes, Bosch-Barrera, Joaquim, Massutí, Bartomeu, García Campelo, Rosario, Sánchez-Hernández, Alfredo, Laura Ortega, Ana, Guirado, Maria, del Barco, Edel, Camps, Carlos, Casal-Rubio, Joaquin, Dómine, Manuel, Angeles Sala, Mª, Padilla, Airam, Luís González Larriba, Jose, and de Asís Aparisi, Francisco

Published
2024
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14. Immunogenicity of COVID-19 vaccines in lung cancer patients

Author

Provencio, Mariano, Estival, Anna, Franco, Fernando, López-Vivanco, Guillermo, Saigí, María, Arasanz, Hugo, Diz, Pilar, Carcereny, Enric, García, Javier, Aguado, Carlos, Mosquera, Joaquín, Iruarrizaga, Eluska, Majem, Margarita, Bosch-Barrera, Joaquim, Mielgo-Rubio, Xavier, Guirado, María, Juan-Vidal, Óscar, Blasco, Ana, Lucía Gozálvez, Clara, Del Barrio, Anabel, De Portugal, Teresa, López-Martín, Ana, Serrano, Gloria, Campos, Begoña, Rubio, Judit, Catot, Silvia, Esteban, Beatriz, Martí-Ciriquian, Juan Luis, del Barco, Edel, and Calvo, Virginia

Published
2023
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15. Machine learning identifies experimental brain metastasis subtypes based on their influence on neural circuits

Author

Sobrino, Cecilia, Ajenjo, Nuria, Artiga, Maria-Jesus, Ortega-Paino, Eva, García-Calvo, Virginia, Pérez-Núñez, Angel, González-León, Pedro, Jiménez-Roldán, Luis, Moreno, Luis Miguel, Esteban, Olga, Sepúlveda, Juan Manuel, Toldos, Oscar, Hernández-Laín, Aurelio, Arenas, Alicia, Blasco, Guillermo, Alén, José Fernández, Zaragoza, Adolfo de la Lama, Núñez, Antía Domínguez, Calero, Lourdes, Valverde, Concepción Fiaño, Piñeiro, Ana González, Delgado López, Pedro David, Pascual, Mar, Ahicart, Gerard Plans, Otín, Begoña Escolano, Sanchez-Aguilera, Alberto, Masmudi-Martín, Mariam, Navas-Olive, Andrea, Baena, Patricia, Hernández-Oliver, Carolina, Priego, Neibla, Cordón-Barris, Lluís, Alvaro-Espinosa, Laura, García, Santiago, Martínez, Sonia, Lafarga, Miguel, Lin, Michael Z, Al-Shahrour, Fátima, Menendez de la Prida, Liset, and Valiente, Manuel

Published
2023
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16. IASIS and BigMedilytics: Towards personalized medicine in Europe

Author

Ruiz, Ernestina Menasalvas, Rodríguez-González, Alejandro, Martín, Consuelo Gonzalo, Zanin, Massimiliano, Tuñas, Juan Manuel, Provencio, Mariano, Torrente, Maria, Franco, Fabio, Calvo, Virginia, and Nuñez, Beatriz

Subjects
Computer Science - Computers and Society
Abstract

One field of application of Big Data and Artificial Intelligence that is receiving increasing attention is the biomedical domain. The huge volume of data that is customary generated by hospitals and pharmaceutical companies all over the world could potentially enable a plethora of new applications. Yet, due to the complexity of such data, this comes at a high cost. We here review the activities of the research group composed by people of the Universidad Polit\'ecnica de Madrid and the Hospital Universitario Puerta de Hierro de Majadahonda, Spain; discuss their activities within two European projects, IASIS and BigMedilytics; and present some initial results.

Published
2018

17. Determination of essential biomarkers in lung cancer: a real-world data study in Spain with demographic, clinical, epidemiological and pathological characteristics

Author

Provencio, Mariano, Cobo, Manuel, Rodriguez-Abreu, Delvys, Calvo, Virginia, Carcereny, Enric, Cantero, Alexandra, Bernabé, Reyes, Benitez, Gretel, Castro, Rafael López, Massutí, Bartomeu, del Barco, Edel, García Campelo, Rosario, Guirado, Maria, Camps, Carlos, Ortega, Ana Laura, González Larriba, Jose Luis, Sánchez, Alfredo, Casal, Joaquín, Sala, M. Angeles, Juan-Vidal, Oscar, Bosch-Barrera, Joaquim, Oramas, Juana, Dómine, Manuel, Trigo, Jose Manuel, Blanco, Remei, Calzas, Julia, Morilla, Idoia, Padilla, Airam, Pimentao, Joao, Sousa, Pedro A., and Torrente, Maria

Published
2022
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18. Perinatal outcomes of pregnancies resulting from assisted reproduction technology in SARS-CoV-2-infected women: a prospective observational study

Author

Garrido Luque, María Belén, Fernández, Camino Fernández, Yarza, Ana Villalba, Canedo Carballeira, Esther María, Dueñas Carazo, María Begoña, Aguilar, Rosario Redondo, Sánchez-Vegazo García, Ángeles, Silvares, Esther Álvarez, Pardo Pumar, María Isabel, Álvarez-Mallo, Macarena Alférez, Carmona, Víctor Muñoz, Pérez, Noelia Pérez, Colomo, Cristina Álvarez, Mateu, Onofre Alomar, Di Leo, Claudio Marañon, Millán, María del Carmen Parada, García, Adrián Martín, Martínez, José Navarrina, Fornell, Anna Mundó, Salvador, Elena Pascual, Gómez, Tania Manrique, Meca Casbas, Marta Ruth, Grimalt, Noemí Freixas, Aquise, Adriana, Gil, María del Mar, Amorós, Eduardo Cazorla, Sánchez, Alberto Armijo, Conca Rodero, María Isabel, Oreja Cuesta, Ana Belén, Aguilar, Cristina Ruiz, García, Susana Fernández, Gómez, Mercedes Ramírez, Aguilar Galán, Esther Vanessa, Pérez, Rocío López, Luque, Carmen Baena, Jiménez Losa, Luz María, Pérez, Susana Soldevilla, Granell Escobar, María Reyes, González, Manuel Domínguez, Blaya, Flora Navarro, Wizner de Alva, Juan Carlos, Carulla, Rosa Pedró, Sánchez, Encarnación Carmona, Rodríguez, Judit Canet, Antolín, Eva Morán, Macià, Montse, Pratcorona, Laia, Abásolo, Irene Gastaca, Borde, Begoña Martínez, Ruiz, Óscar Vaquerizo, Aragón, José Ruiz, Seoane, Raquel González, González, María Teulón, González, Lourdes Martín, Heredia, Cristina Lesmes, Broullón Molanes, J. Román, Gimeno Gimeno, María Joaquina, Posadas San Juan, Alma María, Vanegas, Otilia González, Fernández Alonso, Ana María, Meca, Lucía Díaz, Prieto, Alberto Puerta, Martín, María del Pilar Guadix, Orizales Lago, Carmen María, Sainz Bueno, José Antonio, Coello, Mónica Catalina, José Núñez Valera, María, González, Lucas Cerrillos, García, José Adanez, Ferriols-Pérez, Elena, Roqueta, Marta, Encinas Pardilla, María Begoña, Sánchez, Marta García, Rodríguez, Laura González, Recarte, Pilar Pintado, Paredes, Elena Pintado, Payán, Paola Carmona, Iriarte, Yosu Franco, San Frutos Llorente, Luis, Engels Calvo, Virginia, Cruz Melguizo, Sara, Abascal-Saiz, Alejandra, Forcén Acebal, Laura, Sánchez-Migallón, Amalia, Pintado Recarte, Pilar, Cuenca Marín, Celia, Marcos Puig, Beatriz, Del Barrio Fernández, Pablo G., Nieto Velasco, Olga, de la Cruz Conty, María Luisa, and Martínez-Perez, Oscar

Published
2021
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19. Children with Autism and Picture Books: Extending the Reading Experiences of Autistic Learners of Primary Age

Author

Tabernero, Rosa and Calvo, Virginia

Abstract

Autistic learners master visual and spatial abilities; they use visual language to organise, understand and give meaning to the world. Although they might struggle with verbal skills, they have an associative way of thinking. Taking into consideration the characteristics of seven autistic pupils, the aim of this paper was to identify the potential of picture books in relation to autistic readers in order to explain why picture books can be supportive tools for improving verbal and social communication skills. The findings, based on a qualitative case study and a reader response framework, show that picture books help children with autism develop social and communication skills as well as foster imagination. Their written outcomes clearly showed children's need to tell stories.

Published
2020
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20. High risk of thrombosis in patients with advanced lung cancer harboring rearrangements in ROS1

Author

Muñoz-Unceta, Nerea, Zugazagoitia, Jon, Manzano, Arancha, Jiménez-Aguilar, Elisabeth, Olmedo, María E., Cacho, Juan D., Oliveira, Julio, Dómine, Manuel, Ortega-Morán, Laura, Aguado, Carlos, Luna, Ana M., Fernández, Lourdes, Pérez, Javier, Font, Carme, Salvador, Carmen, Corral, Jesús, Benítez, Gretel, Ros, Silverio, Biosca, Mercedes, Calvo, Virginia, Martínez, Julia, Sánchez-Cánovas, Manuel, López, Rafael, Sereno, María, Mielgo, Xabier, Aparisi, Francisco, Carmona, Marta, Carrión, Rafael, Ponce-Aix, Santiago, Soares, Marta, Martínez-Salas, Imanol, García-Morillo, Marcial, Juan-Vidal, Oscar, Blasco, Ana, Muñoz, Andrés J., and Paz-Ares, Luis

Published
2020
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21. Neoadjuvant chemotherapy and nivolumab in resectable non-small-cell lung cancer (NADIM): an open-label, multicentre, single-arm, phase 2 trial

Author

Provencio, Mariano, Nadal, Ernest, Insa, Amelia, García-Campelo, María Rosario, Casal-Rubio, Joaquín, Dómine, Manuel, Majem, Margarita, Rodríguez-Abreu, Delvys, Martínez-Martí, Alex, De Castro Carpeño, Javier, Cobo, Manuel, López Vivanco, Guillermo, Del Barco, Edel, Bernabé Caro, Reyes, Viñolas, Nuria, Barneto Aranda, Isidoro, Viteri, Santiago, Pereira, Eva, Royuela, Ana, Casarrubios, Marta, Salas Antón, Clara, Parra, Edwin R, Wistuba, Ignacio, Calvo, Virginia, Laza-Briviesca, Raquel, Romero, Atocha, Massuti, Bartomeu, and Cruz-Bermúdez, Alberto

Published
2020
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22. Sex is a strong prognostic factor in stage IV non-small-cell lung cancer patients and should be considered in survival rate estimation

Author

Barquín, Miguel, Calvo, Virginia, García-García, Francisco, Nuñez, Beatriz, Sánchez-Herrero, Estela, Serna-Blasco, Roberto, Auglytė, Milda, Carcereny, Enric, Rodriguez-Abreu, Delvys, López Castro, Rafael, Guirado, María, Camps, Carlos, Bosch-Barrera, Joaquín, Massuti, Bartomeu, Ortega, Ana Laura, del Barco, Edel, Gonzalez-Larriba, José Luis, Aguiar, David, García-Campelo, Rosario, Dómine, Manuel, Agraso, Sara, Sala, Mª Angeles, Oramas, Juana, Bernabé, Reyes, Blanco, Remei, Parejo, Consuelo, Cruz, Alberto, Menasalvas, Ernestina, Royuela, Ana, Romero, Atocha, and Provencio, Mariano

Published
2020
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23. Targeting calciumopathy for neuroprotection: focus on calcium channels Cav1, Orai1 and P2X7

Author

Universidad de Alicante. Departamento de Óptica, Farmacología y Anatomía, Torres, Myriam, García-Calvo, Virginia, Gironda, Adrián, Pascual, Jorge, García, Antonio G., Maneu, Victoria, Universidad de Alicante. Departamento de Óptica, Farmacología y Anatomía, Torres, Myriam, García-Calvo, Virginia, Gironda, Adrián, Pascual, Jorge, García, Antonio G., and Maneu, Victoria

Abstract

As the uncontrolled entry of calcium ions (Ca2+) through plasmalemmal calcium channels is a cell death trigger, the conjecture is here raised that mitigating such an excess of Ca2+ entry should rescue from death the vulnerable neurons in neurodegenerative diseases (NDDs). However, this supposition has failed in some clinical trials (CTs). Thus, a recent CT tested whether isradipine, a blocker of the Cav1 subtype of voltage-operated calcium channels (VOCCs), exerted a benefit in patients with Parkinson's disease (PD); however, outcomes were negative. This is one more of the hundreds of CTs done under the principle of one-drug-one-target, that have failed in Alzheimer's disease (AD) and other NDDs during the last three decades. As there are myriad calcium channels to let Ca2+ ions gain the cell cytosol, it seems reasonable to predict that blockade of Ca2+ entry through a single channel may not be capable of preventing the Ca2+ flood of cells by the uncontrolled Ca2+ entry. Furthermore, as Ca2+ signaling is involved in the regulation of myriad functions in different cell types, it seems also reasonable to guess that a therapy should be more efficient by targeting different cells with various drugs. Here, we propose to mitigate Ca2+ entry by the simultaneous partial blockade of three quite different subtypes of plasmalemmal calcium channels that is, the Cav1 subtype of VOCCs, the Orai1 store-operated calcium channel (SOCC), and the purinergic P2×7 calcium channel. All three channels are expressed in both microglia and neurons. Thus, by targeting the three channels with a combination of three drug blockers we expect favorable changes in some of the pathogenic features of NDDs, namely (i) to mitigate Ca2+ entry into microglia; (ii) to decrease the Ca2+-dependent microglia activation; (iii) to decrease the sustained neuroinflammation; (iv) to decrease the uncontrolled Ca2+ entry into neurons; (v) to rescue vulnerable neurons from death; and (vi) to delay disease progressio

Published
2024

24. Cisplatin resistance involves a metabolic reprogramming through ROS and PGC-1α in NSCLC which can be overcome by OXPHOS inhibition

Author

Cruz-Bermúdez, Alberto, Laza-Briviesca, Raquel, Vicente-Blanco, Ramiro J., García-Grande, Aránzazu, Coronado, Maria José, Laine-Menéndez, Sara, Palacios-Zambrano, Sara, Moreno-Villa, M. Rocío, Ruiz-Valdepeñas, Asunción Martin, Lendinez, Cristina, Romero, Atocha, Franco, Fernando, Calvo, Virginia, Alfaro, Cristina, Acosta, Paloma Martin, Salas, Clara, Garcia, José Miguel, and Provencio, Mariano

Published
2019
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25. A Descriptive Study of 103 Primary Cutaneous B-Cell Lymphomas: Clinical and Pathological Characteristics and Treatment from the Spanish Lymphoma Oncology Group (GOTEL)

Author

Martínez-Banaclocha, Natividad, primary, Martínez-Madueño, Francisca, additional, Caballé, Berta, additional, Badia, Joan, additional, Blanes, Mar, additional, Bujanda, David Aguiar, additional, Calvo, Virginia, additional, Gómez Codina, Jose, additional, Blanco, Cristina Quero, additional, Espinosa, Pablo, additional, Lavernia, Javier, additional, Arroyo, Francisco Ramón García, additional, Risueño, María Guirado, additional, Llorca, Cristina, additional, Cumeras, Raquel, additional, Pulla, Mariano Provencio, additional, and Gumà, Josep, additional

Published
2024
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26. Osimertinib in advanced EGFR-T790M mutation-positive non-small cell lung cancer patients treated within the Special Use Medication Program in Spain: OSIREX-Spanish Lung Cancer Group

Author

Provencio, Mariano, Terrasa, Josefa, Garrido, Pilar, Campelo, Rosario García, Aparisi, Francisco, Diz, Pilar, Aguiar, David, García-Giron, Carlos, Hidalgo, Julia, Aguado, Carlos, González, Jorge García, Esteban, Emilio, Gómez-Aldavarí, Lorenzo, Moran, Teresa, Juan, Oscar, Chara, Luís Enrique, Marti, Juan L., Castro, Rafael López, Ortega, Ana Laura, Moreno, Elia Martínez, Coves, Juan, Sánchez Peña, Ana M., Bosch-Barrera, Joaquim, Gastaldo, Amparo Sánchez, Núñez, Natalia Fernández, del Barco, Edel, Cobo, Manuel, Isla, Dolores, Majem, Margarita, Navarro, Fátima, and Calvo, Virginia

Published
2021
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29. Perioperative Nivolumab and Chemotherapy in Stage III Non–Small-Cell Lung Cancer

Author

Provencio, Mariano, primary, Nadal, Ernest, additional, González-Larriba, José L., additional, Martínez-Martí, Alex, additional, Bernabé, Reyes, additional, Bosch-Barrera, Joaquim, additional, Casal-Rubio, Joaquín, additional, Calvo, Virginia, additional, Insa, Amelia, additional, Ponce, Santiago, additional, Reguart, Noemí, additional, de Castro, Javier, additional, Mosquera, Joaquín, additional, Cobo, Manuel, additional, Aguilar, Andrés, additional, López Vivanco, Guillermo, additional, Camps, Carlos, additional, López-Castro, Rafael, additional, Morán, Teresa, additional, Barneto, Isidoro, additional, Rodríguez-Abreu, Delvys, additional, Serna-Blasco, Roberto, additional, Benítez, Raquel, additional, Aguado de la Rosa, Carlos, additional, Palmero, Ramón, additional, Hernando-Trancho, Florentino, additional, Martín-López, Javier, additional, Cruz-Bermúdez, Alberto, additional, Massuti, Bartomeu, additional, and Romero, Atocha, additional

Published
2023
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30. Machine learning identifies experimental brain metastasis subtypes based on their influence on neural circuits

Author

Sanchez-Aguilera, Alberto, primary, Masmudi-Martín, Mariam, additional, Navas-Olive, Andrea, additional, Baena, Patricia, additional, Hernández-Oliver, Carolina, additional, Priego, Neibla, additional, Cordón-Barris, Lluís, additional, Alvaro-Espinosa, Laura, additional, García, Santiago, additional, Martínez, Sonia, additional, Lafarga, Miguel, additional, Lin, Michael Z, additional, Al-Shahrour, Fátima, additional, Menendez de la Prida, Liset, additional, Valiente, Manuel, additional, Sobrino, Cecilia, additional, Ajenjo, Nuria, additional, Artiga, Maria-Jesus, additional, Ortega-Paino, Eva, additional, García-Calvo, Virginia, additional, Pérez-Núñez, Angel, additional, González-León, Pedro, additional, Jiménez-Roldán, Luis, additional, Moreno, Luis Miguel, additional, Esteban, Olga, additional, Sepúlveda, Juan Manuel, additional, Toldos, Oscar, additional, Laín, Aurelio Hernández, additional, Arenas, Alicia, additional, Blasco, Guillermo, additional, Alén, José Fernández, additional, Zaragoza, Adolfo de la Lama, additional, Núñez, Antía Domínguez, additional, Calero, Lourdes, additional, Valverde, Concepción Fiaño, additional, Piñeiro, Ana González, additional, Delgado López, Pedro David, additional, Pascual, Mar, additional, Ahicart, Gerard Plans, additional, and Otín, Begoña Escolano, additional

Published
2023
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32. Monitoring with circulating tumor cells in the perioperative setting of patients with surgically treated stages I–IIIA NSCLC

Author

Garitaonaindia, Yago, primary, Aguado-Noya, Ramón, additional, Garcia-Grande, Aranzazu, additional, Cordoba, Mar, additional, Coronado Albi, Maria Jose, additional, Campo Cañaveral, Jose Luis, additional, Calvo, Virginia, additional, Clemente, Mariola Blanco, additional, Álvarez, Ruth, additional, Peñas, Marta, additional, Chara, Luis, additional, Royuela, Ana, additional, and Provencio, Mariano, additional

Published
2023
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34. Machine Learning Survival Models for Relapse Prediction in a Early Stage Lung Cancer Patient

Author

Timilsina, Mohan, primary, Buosi, Samuele, additional, Janik, Adrianna, additional, Minervini, Pasquale, additional, Costabello, Luca, additional, Torrente, Maria, additional, Provencio, Mariano, additional, Calvo, Virginia, additional, Camps, Carlos, additional, Ortega, Ana L., additional, Massutí, Bartomeu, additional, Campelo, M.Rosario Garcia, additional, del Barco, Edel, additional, Bosch-Barrera, Joaquim, additional, and Novacek, Vit, additional

Published
2023
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35. DetectingALK,ROS1andRETfusions and theMETΔex14splicing variant in liquid biopsies of non‐small cell lung cancer patients using RNA ‐based techniques

Author

Giménez‐Capitán, Ana, primary, Sánchez‐Herrero, Estela, additional, Robado de Lope, Lucía, additional, Aguilar‐Hernández, Andrés, additional, Sullivan, Ivana, additional, Calvo, Virginia, additional, Moya‐Horno, Irene, additional, Viteri, Santiago, additional, Cabrera, Carlos, additional, Aguado, Cristina, additional, Armiger, Noelia, additional, Valarezo, Joselyn, additional, Mayo‐de‐las‐Casas, Clara, additional, Reguart, Noemí, additional, Rosell, Rafael, additional, Provencio, Mariano, additional, Romero, Atocha, additional, and Molina‐Vila, Miguel A., additional

Published
2023
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36. Data from Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study

Author

Fernández-Miranda, Ismael, primary, Pedrosa, Lucía, primary, Llanos, Marta, primary, Franco, Fernando F., primary, Gómez, Sagrario, primary, Martín-Acosta, Paloma, primary, García-Arroyo, Francisco R., primary, Gumá, Josep, primary, Horcajo, Beatriz, primary, Ballesteros, Ana K., primary, Gálvez, Laura, primary, Martínez, Natividad, primary, Marín, Miguel, primary, Sequero, Silvia, primary, Navarro, Marta, primary, Yanguas-Casás, Natalia, primary, Calvo, Virginia, primary, Rueda-Domínguez, Antonio, primary, Provencio, Mariano, primary, and Sánchez-Beato, Margarita, primary

Published
2023
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37. Supplementary Data 2 from Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study

Author

Fernández-Miranda, Ismael, primary, Pedrosa, Lucía, primary, Llanos, Marta, primary, Franco, Fernando F., primary, Gómez, Sagrario, primary, Martín-Acosta, Paloma, primary, García-Arroyo, Francisco R., primary, Gumá, Josep, primary, Horcajo, Beatriz, primary, Ballesteros, Ana K., primary, Gálvez, Laura, primary, Martínez, Natividad, primary, Marín, Miguel, primary, Sequero, Silvia, primary, Navarro, Marta, primary, Yanguas-Casás, Natalia, primary, Calvo, Virginia, primary, Rueda-Domínguez, Antonio, primary, Provencio, Mariano, primary, and Sánchez-Beato, Margarita, primary

Published
2023
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38. Supplementary Data 1 from Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study

Author

Fernández-Miranda, Ismael, primary, Pedrosa, Lucía, primary, Llanos, Marta, primary, Franco, Fernando F., primary, Gómez, Sagrario, primary, Martín-Acosta, Paloma, primary, García-Arroyo, Francisco R., primary, Gumá, Josep, primary, Horcajo, Beatriz, primary, Ballesteros, Ana K., primary, Gálvez, Laura, primary, Martínez, Natividad, primary, Marín, Miguel, primary, Sequero, Silvia, primary, Navarro, Marta, primary, Yanguas-Casás, Natalia, primary, Calvo, Virginia, primary, Rueda-Domínguez, Antonio, primary, Provencio, Mariano, primary, and Sánchez-Beato, Margarita, primary

Published
2023
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39. Long‐term outcomes in Hodgkin lymphoma survivors. Temporary trends and comparison with general population

Author

Núñez‐García, Beatriz, primary, Clemente, Mariola Blanco, additional, Sánchez, Juan Cristóbal, additional, Royuela, Ana, additional, Ibargüen, Blanca Cantos Sánchez de, additional, Méndez, Miriam, additional, López‐Ibor, Jorge V., additional, Martínez, Marta, additional, Traseira, Cristina, additional, Garitaonaindia, Yago, additional, Aguado, Ramón, additional, Calvo, Virginia, additional, Torrente, María, additional, Parejo, Consuelo, additional, Provencio, Zaida, additional, and Provencio, Mariano, additional

Published
2023
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40. Atezolizumab Plus Bevacizumab as First-line Treatment for Patients With Metastatic Nonsquamous Non–Small Cell Lung Cancer With High Tumor Mutation Burden

Author

Provencio, Mariano, primary, Ortega, Ana Laura, additional, Coves-Sarto, Juan, additional, Calvo, Virginia, additional, Marsé-Fabregat, Raquel, additional, Dómine, Manuel, additional, Guirado, María, additional, Carcereny, Enric, additional, Fernández, Natalia, additional, Álvarez, Ruth, additional, Blanco, Remei, additional, León-Mateos, Luis, additional, Sánchez-Torres, José Miguel, additional, Sullivan, Ivana Gabriela, additional, Cobo, Manuel, additional, Sánchez-Hernández, Alfredo, additional, Massuti, Bartomeu, additional, Sierra-Rodero, Belen, additional, Mártinez-Toledo, Cristina, additional, Serna-Blasco, Roberto, additional, Romero, Atocha, additional, and Cruz-Bermúdez, Alberto, additional

Published
2023
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42. Assessing the risk of cardiovascular events in patients receiving immune checkpoint inhibitors

Author

Torrente, María, primary, Blanco, Mariola, additional, Franco, Fabio, additional, Garitaonaindia, Yago, additional, Calvo, Virginia, additional, Collazo-Lorduy, Ana, additional, Gutiérrez, Lourdes, additional, Sánchez, Juan Cristóbal, additional, González-del-Alba, Aranzazu, additional, Hernández, Roberto, additional, Méndez, Miriam, additional, Cantos, Blanca, additional, Núñez, Beatriz, additional, Sousa, Pedro A. C., additional, and Provencio, Mariano, additional

Published
2022
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43. Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study

Author

Fernández-Miranda, Ismael, primary, Pedrosa, Lucía, additional, Llanos, Marta, additional, Franco, Fernando F., additional, Gómez, Sagrario, additional, Martín-Acosta, Paloma, additional, García-Arroyo, Francisco R., additional, Gumá, Josep, additional, Horcajo, Beatriz, additional, Ballesteros, Ana K., additional, Gálvez, Laura, additional, Martínez, Natividad, additional, Marín, Miguel, additional, Sequero, Silvia, additional, Navarro, Marta, additional, Yanguas-Casás, Natalia, additional, Calvo, Virginia, additional, Rueda-Domínguez, Antonio, additional, Provencio, Mariano, additional, and Sánchez-Beato, Margarita, additional

Published
2022
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47. Prognostic value of event‐free survival at 12 and 24 months and long‐term mortality for non‐Hodgkin follicular lymphoma patients: A study report from the Spanish Lymphoma Oncology Group

Author

Provencio, Mariano, Royuela, Ana, Torrente, María, Pollán, Marina, Gómez‐Codina, José, Sabín, Pilar, Llanos, Marta, Gumá, Josep, Quero, Cristina, Blasco, Ana, Aguiar, David, García‐Arroyo, Francisco Ramón, Lavernia, Javier, Martínez, Natividad, Morales, Manuel, Saenz‐Cusi, Álvaro, Rodríguez, Delvys, Calvo, Virginia, de la Cruz‐Merino, Luis, de la Cruz, Miguel Ángel, and Rueda, Antonio

Published
2017
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48. Detecting ALK, ROS1, and RET fusions and the METΔex14 splicing variant in liquid biopsies of non‐small‐cell lung cancer patients using RNA‐based techniques.

Author

Giménez‐Capitán, Ana, Sánchez‐Herrero, Estela, Robado de Lope, Lucía, Aguilar‐Hernández, Andrés, Sullivan, Ivana, Calvo, Virginia, Moya‐Horno, Irene, Viteri, Santiago, Cabrera, Carlos, Aguado, Cristina, Armiger, Noelia, Valarezo, Joselyn, Mayo‐de‐las‐Casas, Clara, Reguart, Noemí, Rosell, Rafael, Provencio, Mariano, Romero, Atocha, and Molina‐Vila, Miguel A.

Abstract

ALK, ROS1, and RET fusions and MET∆ex14 variant associate with response to targeted therapies in non‐small‐cell lung cancer (NSCLC). Technologies for fusion testing in tissue must be adapted to liquid biopsies, which are often the only material available. In this study, circulating‐free RNA (cfRNA) and extracellular vesicle RNA (EV‐RNA) were purified from liquid biopsies. Fusion and MET∆ex14 transcripts were analyzed by nCounter (Nanostring) and digital PCR (dPCR) using the QuantStudio® System (Applied Biosystems). We found that nCounter detected ALK, ROS1, RET, or MET∆ex14 aberrant transcripts in 28/40 cfRNA samples from positive patients and 0/16 of control individuals (70% sensitivity). Regarding dPCR, aberrant transcripts were detected in the cfRNA of 25/40 positive patients. Concordance between the two techniques was 58%. Inferior results were obtained when analyzing EV‐RNA, where nCounter often failed due to a low amount of input RNA. Finally, results of dPCR testing in serial liquid biopsies of five patients correlated with response to targeted therapy. We conclude that nCounter can be used for multiplex detection of fusion and MET∆ex14 transcripts in liquid biopsies, showing a performance comparable with next‐generation sequencing platforms. dPCR could be employed for disease follow‐up in patients with a known alteration. cfRNA should be preferred over EV‐RNA for these analyses. [ABSTRACT FROM AUTHOR]

Published
2023
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49. Machine Learning–Assisted Recurrence Prediction for Patients With Early-Stage Non–Small-Cell Lung Cancer.

Author

Janik, Adrianna, Torrente, Maria, Costabello, Luca, Calvo, Virginia, Walsh, Brian, Camps, Carlos, Mohamed, Sameh K., Ortega, Ana L., Nováček, Vít, Massutí, Bartomeu, Minervini, Pasquale, Campelo, M. Rosario Garcia, del Barco, Edel, Bosch-Barrera, Joaquim, Menasalvas, Ernestina, Timilsina, Mohan, and Provencio, Mariano

Subjects
NON-small-cell lung carcinoma, DISEASE relapse, MACHINE learning, CANCER patients, LUNG cancer, RESEARCH questions, PROGRESSION-free survival
Abstract

PURPOSE: Stratifying patients with cancer according to risk of relapse can personalize their care. In this work, we provide an answer to the following research question: How to use machine learning to estimate probability of relapse in patients with early-stage non–small-cell lung cancer (NSCLC)? MATERIALS AND METHODS: For predicting relapse in 1,387 patients with early-stage (I-II) NSCLC from the Spanish Lung Cancer Group data (average age 65.7 years, female 24.8%, male 75.2%), we train tabular and graph machine learning models. We generate automatic explanations for the predictions of such models. For models trained on tabular data, we adopt SHapley Additive exPlanations local explanations to gauge how each patient feature contributes to the predicted outcome. We explain graph machine learning predictions with an example-based method that highlights influential past patients. RESULTS: Machine learning models trained on tabular data exhibit a 76% accuracy for the random forest model at predicting relapse evaluated with a 10-fold cross-validation (the model was trained 10 times with different independent sets of patients in test, train, and validation sets, and the reported metrics are averaged over these 10 test sets). Graph machine learning reaches 68% accuracy over a held-out test set of 200 patients, calibrated on a held-out set of 100 patients. CONCLUSION: Our results show that machine learning models trained on tabular and graph data can enable objective, personalized, and reproducible prediction of relapse and, therefore, disease outcome in patients with early-stage NSCLC. With further prospective and multisite validation, and additional radiological and molecular data, this prognostic model could potentially serve as a predictive decision support tool for deciding the use of adjuvant treatments in early-stage lung cancer. [ABSTRACT FROM AUTHOR]

Published
2023
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50. Incidence of chemotherapy-induced nausea and vomiting with moderately emetogenic chemotherapy: ADVICE (Actual Data of Vomiting Incidence by Chemotherapy Evaluation) study

Author

Escobar, Yolanda, Cajaraville, Gerardo, Virizuela, Juan Antonio, Álvarez, Rosa, Muñoz, Andrés, Olariaga, Olatz, Tamés, María José, Muros, Begoña, Lecumberri, María Jose, Feliu, Jaime, Martínez, Purificación, Adansa, Juan Carlos, Martínez, María José, López, Rafael, Blasco, Ana, Gascón, Pere, Calvo, Virginia, Luna, Pablo, Montalar, Joaquín, Del Barrio, Patricia, and Tornamira, María Victoria

Published
2015
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