Search

Your search keyword '"Cuesta, Isabel"' showing total 414 results
Start Over Author "Cuesta, Isabel"
414 results on '"Cuesta, Isabel"'

1. Monkeypox virus genomic accordion strategies

Author

Monzón, Sara, Varona, Sarai, Negredo, Anabel, Vidal-Freire, Santiago, Patiño-Galindo, Juan Angel, Ferressini-Gerpe, Natalia, Zaballos, Angel, Orviz, Eva, Ayerdi, Oskar, Muñoz-Gómez, Ana, Delgado-Iribarren, Alberto, Estrada, Vicente, García, Cristina, Molero, Francisca, Sánchez-Mora, Patricia, Torres, Montserrat, Vázquez, Ana, Galán, Juan-Carlos, Torres, Ignacio, Causse del Río, Manuel, Merino-Diaz, Laura, López, Marcos, Galar, Alicia, Cardeñoso, Laura, Gutiérrez, Almudena, Loras, Cristina, Escribano, Isabel, Alvarez-Argüelles, Marta E., del Río, Leticia, Simón, María, Meléndez, María Angeles, Camacho, Juan, Herrero, Laura, Jiménez, Pilar, Navarro-Rico, María Luisa, Jado, Isabel, Giannetti, Elaina, Kuhn, Jens H., Sanchez-Lockhart, Mariano, Di Paola, Nicholas, Kugelman, Jeffrey R., Guerra, Susana, García-Sastre, Adolfo, Cuesta, Isabel, Sánchez-Seco, Maripaz P., and Palacios, Gustavo

Published
2024
Full Text
View/download PDF

3. Monkeypox outbreak in Madrid (Spain): Clinical and virological aspects

Author

Ballesteros, Juan, Baza, Begoña, Carrió, Juan Carlos, Chocron, Cynthia, Fedele, Giovanni, García-Amil, Cristina, Herrero, Laura, Homen, Reynaldo, Mariano, Alberto, Martínez-Burgoa, Teresa, Molero, Francisca, Navarro, Maria Luisa, Núñez, Maria José, Perez-Somarriba, Juncal, Puerta, Teresa, Rodríguez-Añover, Javier, Pastrana, Esperanza Pérez, Jiménez, Mercedes, de la Vega, Leticia, Vergas, Jorge, Zarza, Isabel, Orviz, Eva, Negredo, Anabel, Ayerdi, Oskar, Vázquez, Ana, Muñoz-Gomez, Ana, Monzón, Sara, Clavo, Petunia, Zaballos, Angel, Vera, Mar, Sánchez, Patricia, Cabello, Noemi, Jiménez, Pilar, Pérez-García, Jorge A., Varona, Sarai, del Romero, Jorge, Cuesta, Isabel, Delgado-Iribarren, Alberto, Torres, Montse, Sagastagoitia, Iñigo, Palacios, Gustavo, Estrada, Vicente, and Sánchez-Seco, Maria Paz

Published
2022
Full Text
View/download PDF

4. Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant

Author

Boer, Elke de, Cohen, Enzo, Cuesta, Isabel, Danis, Daniel, Denommé-Pichon, Anne-Sophie, Gao, Fei, Gilissen, Christian, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Matalonga, Leslie, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, Paske, Iris B.A.W. te, Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, Trimouille, Aurélien, van der Velde, Joeri K., Vandrovcova, Jana, Vitobello, Antonio, Zurek, Birte, Abbot, Kristin M., Banka, Siddharth, Benetti, Elisa, de Boer, Elke, Casari, Giorgio, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Ellwanger, Kornelia, Faivre, Laurence, Graessner, Holm, Haack, Tobias B., Hammarsjö, Anna, Havlovicova, Marketa, Hoischen, Alexander, Hugon, Anne, Jackson, Adam, Kerstjens, Mieke, Kleefstra, Tjitske, Lindstrand, Anna, Martín, Estrella López, Macek, Milan, Jr., Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Nordgren, Ann, Pettersson, Maria, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca C., Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Santen, Gijs W.E., Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Verloes, Alain, Vissers, Lisenka, Votypka, Pavel, Vyshka, Klea, Zguro, Kristina, Yaldiz, Burcu, Laurie, Steve, de Reuver, Rick, Kwint, Michael, Pfundt, Rolph, Willemsen, Michèl A.A.P., Vries, Bert B.A. de, Vitobello, A., and Vissers, Lisenka E.L.M.

Published
2022
Full Text
View/download PDF

9. Absceso hepático por espina de pescado: reporte de caso.

Author

Aileen Cuesta-Pertuz, Annar, Alberto Mosquera-López, Óscar, Cristina Palacios-Cuesta, Isabel, Alberto Mosquera-López, Jesús, and Patricia De León-Valdés, Daniela

Abstract

Copyright of Revista Colombiana de Gastroenterología is the property of Asociacion Colombiana de Gastroenterologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2024
Full Text
View/download PDF

10. Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences

Author

Iglesias-Caballero, María, primary, Camarero-Serrano, Sara, additional, Varona, Sarai, additional, Mas, Vicente, additional, Calvo, Cristina, additional, García, María Luz, additional, García-Costa, Juan, additional, Vázquez-Morón, Sonia, additional, Monzón, Sara, additional, Campoy, Albert, additional, Cuesta, Isabel, additional, Pozo, Francisco, additional, and Casas, Inmaculada, additional

Published
2023
Full Text
View/download PDF

11. Frequency of low-level and high-level mosaicism in sporadic retinoblastoma: genotype–phenotype relationships

Author

Rodríguez-Martín, Carlos, Robledo, Cristina, Gómez-Mariano, Gema, Monzón, Sara, Sastre, Ana, Abelairas, Jose, Sábado, Constantino, Martín-Begué, Nieves, Ferreres, Joan Carles, Fernández-Teijeiro, Ana, González-Campora, Ricardo, Rios-Moreno, María José, Zaballos, Ángel, Cuesta, Isabel, Martínez-Delgado, Beatriz, Posada, Manuel, and Alonso, Javier

Published
2020
Full Text
View/download PDF

13. FAIR+E pathogen data for surveillance and research: lessons from COVID-19

Author

Neves, Aitana, primary, Cuesta, Isabel, additional, Hjerde, Erik, additional, Klemetsen, Terje, additional, Salgado, David, additional, van Helden, Jacques, additional, Rahman, Nadim, additional, Fatima, Nazeefa, additional, Karathanasis, Nestoras, additional, Zmora, Pawel, additional, Åkerström, Wolmar Nyberg, additional, Grellscheid, Sushma Nagaraja, additional, Waheed, Zahra, additional, and Blomberg, Niklas, additional

Published
2023
Full Text
View/download PDF

15. Quantitative Lipid Profiling Reveals Major Differences between Liver Organoids with Normal Pi*M and Deficient Pi*Z Variants of Alpha-1-antitrypsin

Author

Pérez-Luz, Sara, primary, Lalchandani, Jaanam, additional, Matamala, Nerea, additional, Barrero, Maria Jose, additional, Gil-Martín, Sara, additional, Saz, Sheila Ramos-Del, additional, Varona, Sarai, additional, Monzón, Sara, additional, Cuesta, Isabel, additional, Justo, Iago, additional, Marcacuzco, Alberto, additional, Hierro, Loreto, additional, Garfia, Cristina, additional, Gomez-Mariano, Gema, additional, Janciauskiene, Sabina, additional, and Martínez-Delgado, Beatriz, additional

Published
2023
Full Text
View/download PDF

16. FAIR+E Pathogen data for surveillance and research: lessons from COVID-19

Author

Neves, Aitana, Cuesta, Isabel, Hjerde, Erik, Salgado, David, van Helden, Jacques, Rahman, Nadim, Fatima, Nazeefa, Karathanasis, Nestoras, Zmora, Pawel, Nyberg Åkerström, Wolmar, Nagaraja Grellscheid, Sushma, Waheed, Zahra, Blomberg, Niklas, and ELIXIR CONVERGE WP9 community

Subjects
pathogen data sharing
Abstract

The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organisational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy towards addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To get started in these challenging endeavors, we started an ELIXIR Focus Group and invite all interested experts to join in this concerted, expert-driven effort towards sustaining and ensuring high-quality data for global surveillance and research.

Published
2023
Full Text
View/download PDF

17. ELIXIR-CONVERGE D9.2 Document where code from the various regional/national data hubs is available; training documentation on data submission by the platforms - relates to tasks 9.1-9.2

Author

Neves, Aitana, Dolanski-Aghamanoukjan, Lorenz, Maier, Wolfgang, Pergl, Robert, Akerström, Wolmar Nyberg, Hjerde, Erik, Cuesta, Isabel, Popleteeva, Marina, Oulas, Anastasia, Mohamed, Anliat, Tonazzolli, Arianna, Pilvar, Diana, Calhoun, Erin, Åberg, Espen, Erard, Frédéric, Rasche, Helena, Messak, Imane, van Helden, Jacques, Lara, Maria, Rahman, Nadim, Karathanasis, Nestoras, Willassen, Nils-Peder, Zmora, Pawel, Monzón, Sara, Hiltemann, Saskia, Singhroha, Sunny, Klemetsen, Terje, Denecker, Thomas, and Waheed, Zahra

Subjects
COVID-19 Data Platform, RDMKit, COVID-19, SARS-COV-2, data brokering, ELIXIR-CONVERGE, COVID-19 Data Portal, ELIXIR
Abstract

Deliverable 9.2 relates to tasks 9.1 and 9.2 on strengthening the central Covid-19 Data Portal and coordinating nascent and established data hubs in mobilising data into the central portal. To achieve this, an active network of regional and national SARS-CoV-2 data hubs managers was established. To get existing data flowing, we first organised a technical workshop on data brokering to the ENA, from which an online tutorial and RDMkit documentation were published. Then, in order to support nascent and more established nodes in mobilising data, we started addressing the various challenges and gaps identified: (i) Importance to build a case for the regional/national data hub and brokering model, also for mid- and long-term funding: a survey was conducted on 11 countries to identify use cases, funding mechanisms and assess sustainability of the developed infrastructures and tools. We aim to publish it in F1000 (ELIXIR Gateway); (ii) Maturity assessment to oversee data hub development and identify potential areas of improvement: a maturity model for pathogen data hubs was developed and is readily available online. (iii) Sensitive data remains siloed and not shared on public open data repositories, calling for the need to federate pathogen data hubs through a central system enabling privacy-preserving data queries and controlled data access following FAIR principles: an opinion paper is being finalised to present and discuss a model of Federated One Health Surveillance Platforms, beyond Covid-19. A proof-of-concept of how a data hub might be “fairified” was also conducted in the Czech Republic. (iv) Training in analytical pipelines and documentation - several actively followed workshops were organised on Galaxy and available pipelines and tools have been documented. (v) Need to better understand the legal aspects of SARS-CoV-2 data sharing: a dedicated workshop was organised to identify the common needs and start addressing them. Legal experts should be further invited to the table given the many open questions remaining. The pandemic has demonstrated the importance of genomic surveillance. This deliverable establishes the foundations to strengthen SARS-CoV-2 data hubs and importantly, scale and expand them to other pathogens and use cases serving both research and surveillance through a federation of hubs.

Published
2023
Full Text
View/download PDF

18. Re-Emergence of a West Nile Virus (WNV) Variant in South Spain with Rapid Spread Capacity

Author

Junta de Andalucía, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Instituto de Salud Carlos III, CSIC - Plataforma Temática Interdisciplinar del CSIC Salud Global (PTI Salud Global), Ruiz-López, María José, Aguilera-Sepúlveda, Pilar, Cebrián-Camisón, Sonia, Figuerola, Jordi, Magallanes, Sergio, Varona, Sarai, Cuesta, Isabel, Cano-Gómez, Cristina, Sánchez-Mora, Patricia, Camacho, Juan, Sánchez-Peña, Carolina, Marchena, Francisco José, Ameyugo, Ulises, Ruiz, Santiago, Sánchez-Seco, María Paz, Agüero, Montserrat, Jiménez-Clavero, Miguel Ángel, Fernández-Pinero, Jovita, Vázquez, Ana, Junta de Andalucía, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Instituto de Salud Carlos III, CSIC - Plataforma Temática Interdisciplinar del CSIC Salud Global (PTI Salud Global), Ruiz-López, María José, Aguilera-Sepúlveda, Pilar, Cebrián-Camisón, Sonia, Figuerola, Jordi, Magallanes, Sergio, Varona, Sarai, Cuesta, Isabel, Cano-Gómez, Cristina, Sánchez-Mora, Patricia, Camacho, Juan, Sánchez-Peña, Carolina, Marchena, Francisco José, Ameyugo, Ulises, Ruiz, Santiago, Sánchez-Seco, María Paz, Agüero, Montserrat, Jiménez-Clavero, Miguel Ángel, Fernández-Pinero, Jovita, and Vázquez, Ana

Abstract

West Nile Virus (WNV) is a mosquito vector-borne zoonosis with an increasing incidence in Europe that has become a public health concern. In Spain, although local circulation has been known for decades, until 2020, when a large outbreak occurred, West Nile Virus cases were scarce and mostly occurred in southern Spain. Since then, there have been new cases every year and the pathogen has spread to new regions. Thus, monitoring of circulating variants and lineages plays a fundamental role in understanding WNV evolution, spread and dynamics. In this study, we sequenced WNV consensus genomes from mosquito pools captured in 2022 as part of a newly implemented surveillance program in southern Spain and compared it to other European, African and Spanish sequences. Characterization of WNV genomes in mosquitoes captured in 2022 reveals the co-circulation of two WNV lineage 1 variants, the one that caused the outbreak in 2020 and another variant that is closely related to variants reported in Spain in 2012, France in 2015, Italy in 2021–2022 and Senegal in 2012–2018. The geographic distribution of these variants indicates that WNV L1 dynamics in southern Europe include an alternating dominance of variants in some territories.

Published
2023

19. Comparing genomic variant identification protocols for Candida auris

Author

Li, Xiao, Muñoz, José F, Gade, Lalitha, Argimon, Silvia, Bougnoux, Marie-Elisabeth, Bowers, Jolene R, Chow, Nancy A, Cuesta, Isabel, Farrer, Rhys A, Maufrais, Corinne, Monroy-Nieto, Juan, Pradhan, Dibyabhaba, Uehling, Jessie, Vu, Duong, Yeats, Corin A, Aanensen, David M, d'Enfert, Christophe, Engelthaler, David M, Eyre, David W, Fisher, Matthew C, Hagen, Ferry, Meyer, Wieland, Singh, Gagandeep, Alastruey-Izquierdo, Ana, Litvintseva, Anastasia P, Cuomo, Christina A, Li, Xiao, Muñoz, José F, Gade, Lalitha, Argimon, Silvia, Bougnoux, Marie-Elisabeth, Bowers, Jolene R, Chow, Nancy A, Cuesta, Isabel, Farrer, Rhys A, Maufrais, Corinne, Monroy-Nieto, Juan, Pradhan, Dibyabhaba, Uehling, Jessie, Vu, Duong, Yeats, Corin A, Aanensen, David M, d'Enfert, Christophe, Engelthaler, David M, Eyre, David W, Fisher, Matthew C, Hagen, Ferry, Meyer, Wieland, Singh, Gagandeep, Alastruey-Izquierdo, Ana, Litvintseva, Anastasia P, and Cuomo, Christina A

Abstract

Genomic analyses are widely applied to epidemiological, population genetic and experimental studies of pathogenic fungi. A wide range of methods are employed to carry out these analyses, typically without including controls that gauge the accuracy of variant prediction. The importance of tracking outbreaks at a global scale has raised the urgency of establishing high-accuracy pipelines that generate consistent results between research groups. To evaluate currently employed methods for whole-genome variant detection and elaborate best practices for fungal pathogens, we compared how 14 independent variant calling pipelines performed across 35 Candida auris isolates from 4 distinct clades and evaluated the performance of variant calling, single-nucleotide polymorphism (SNP) counts and phylogenetic inference results. Although these pipelines used different variant callers and filtering criteria, we found high overall agreement of SNPs from each pipeline. This concordance correlated with site quality, as SNPs discovered by a few pipelines tended to show lower mapping quality scores and depth of coverage than those recovered by all pipelines. We observed that the major differences between pipelines were due to variation in read trimming strategies, SNP calling methods and parameters, and downstream filtration criteria. We calculated specificity and sensitivity for each pipeline by aligning three isolates with chromosomal level assemblies and found that the GATK-based pipelines were well balanced between these metrics. Selection of trimming methods had a greater impact on SAMtools-based pipelines than those using GATK. Phylogenetic trees inferred by each pipeline showed high consistency at the clade level, but there was more variability between isolates from a single outbreak, with pipelines that used more stringent cutoffs having lower resolution. This project generated two truth datasets useful for routine benchmarking of C. auris variant calling, a consensus VCF of g

Published
2023

20. Re-Emergence of a West Nile Virus (WNV) Variant in South Spain with Rapid Spread Capacity.

Author

Ruiz-López, María José, Aguilera-Sepúlveda, Pilar, Cebrián-Camisón, Sonia, Figuerola, Jordi, Magallanes, Sergio, Varona, Sarai, Cuesta, Isabel, Cano-Gómez, Cristina, Sánchez-Mora, Patricia, Camacho, Juan, Sánchez-Peña, Carolina, Marchena, Francisco José, Ameyugo, Ulises, Ruíz, Santiago, Sánchez-Seco, María Paz, Agüero, Montserrat, Jiménez-Clavero, Miguel Ángel, Fernández-Pinero, Jovita, and Vázquez, Ana

Subjects
WEST Nile virus, MOSQUITO vectors, WEST Nile fever, MOSQUITO control, PUBLIC health, ZOONOSES, MOSQUITOES
Abstract

West Nile Virus (WNV) is a mosquito vector-borne zoonosis with an increasing incidence in Europe that has become a public health concern. In Spain, although local circulation has been known for decades, until 2020, when a large outbreak occurred, West Nile Virus cases were scarce and mostly occurred in southern Spain. Since then, there have been new cases every year and the pathogen has spread to new regions. Thus, monitoring of circulating variants and lineages plays a fundamental role in understanding WNV evolution, spread and dynamics. In this study, we sequenced WNV consensus genomes from mosquito pools captured in 2022 as part of a newly implemented surveillance program in southern Spain and compared it to other European, African and Spanish sequences. Characterization of WNV genomes in mosquitoes captured in 2022 reveals the co-circulation of two WNV lineage 1 variants, the one that caused the outbreak in 2020 and another variant that is closely related to variants reported in Spain in 2012, France in 2015, Italy in 2021–2022 and Senegal in 2012–2018. The geographic distribution of these variants indicates that WNV L1 dynamics in southern Europe include an alternating dominance of variants in some territories. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

21. Comparing genomic variant identification protocols for Candida auris

Author

Li, Xiao, primary, Muñoz, José F., additional, Gade, Lalitha, additional, Argimon, Silvia, additional, Bougnoux, Marie-Elisabeth, additional, Bowers, Jolene R., additional, Chow, Nancy A., additional, Cuesta, Isabel, additional, Farrer, Rhys A., additional, Maufrais, Corinne, additional, Monroy-Nieto, Juan, additional, Pradhan, Dibyabhaba, additional, Uehling, Jessie, additional, Vu, Duong, additional, Yeats, Corin A., additional, Aanensen, David M., additional, d’Enfert, Christophe, additional, Engelthaler, David M., additional, Eyre, David W., additional, Fisher, Matthew C., additional, Hagen, Ferry, additional, Meyer, Wieland, additional, Singh, Gagandeep, additional, Alastruey-Izquierdo, Ana, additional, Litvintseva, Anastasia P., additional, and Cuomo, Christina A., additional

Published
2023
Full Text
View/download PDF

23. Genomic Analysis of West Nile Virus Lineage 1 Detected in Mosquitoes during the 2020–2021 Outbreaks in Andalusia, Spain

Author

Ruiz-López, María José, primary, Muñoz-Chimeno, Milagros, additional, Figuerola, Jordi, additional, Gavilán, Ana M., additional, Varona, Sarai, additional, Cuesta, Isabel, additional, Martínez-de la Puente, Josué, additional, Zaballos, Ángel, additional, Molero, Francisca, additional, Soriguer, Ramón C., additional, Sánchez-Seco, Maria Paz, additional, Ruiz, Santiago, additional, and Vázquez, Ana, additional

Published
2023
Full Text
View/download PDF

25. A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis

Author

de Boer, Elke, Ockeloen, Charlotte W., Matalonga, Leslie, Horvath, Rita, Cohen, Enzo, Cuesta, Isabel, Danis, Daniel, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Gilissen, Christian, Johari, Mridul, Laurie, Steven, Li, Shuang, Nelson, Isabelle, Peters, Sophia, Paramonov, Ida, Prasanth, Sivakumar, Robinson, Peter, Sablauskas, Karolis, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vitobello, Antonio, Rodenburg, Richard J., Coenen, Marieke J. H., Janssen, Mirian, Henssen, Dylan, Banka, Siddharth, Benetti, Elisa, Casari, Giorgio, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Ellwanger, Kornelia, Faivre, Laurence, Graessner, Holm, Haack, Tobias B., Hammarsjö, Anna, Havlovicova, Marketa, Hoischen, Alexander, Hugon, Anne, Jackson, Adam, Kleefstra, Tjitske, Lindstrand, Anna, López-Martín, Estrella, Macek, Milan, Morleo, Manuela, Nigro, Vicenzo, Nordgren, Ann, Pettersson, Maria, Pinelli, Michele, Pizzi, Simone, Posada, Manuel, Radio, Francesca Clementina, Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Schwarz, Martin, Tartaglia, Marco, Thauvin, Christel, Torella, Annalaura, Verloes, Alain, Vissers, Lisenka, Votypka, Pavel, Vyshka, Klea, Zurek, Birte, Trimouille, Aurélien, Vissers, Lisenka E. L. M., Laboratoire Maladies Rares: Génétique et Métabolisme (Bordeaux) (U1211 INSERM/MRGM), Université de Bordeaux (UB)-Groupe hospitalier Pellegrin-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de génétique [Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), European Research Council, Evelyn Trust, Newton Fund, European Project: 825619,AI4EU, Dutch Research Council (Holanda), Medical Research Council (Reino Unido), Lily Foundation, Unión Europea. Comisión Europea. H2020, Ockeloen, Charlotte W [0000-0003-0329-1520], Horvath, Rita [0000-0002-9841-170X], Rodenburg, Richard J [0000-0001-5227-3527], Gilissen, Christian [0000-0003-1693-9699], Steyaert, Wouter [0000-0001-8393-0788], Trimouille, Aurélien [0000-0002-3457-5684], Verloes, Alain [0000-0003-4819-0264], Vissers, Lisenka ELM [0000-0001-6470-5497], Apollo - University of Cambridge Repository, de Boer, E., Ockeloen, C. W., Matalonga, L., Horvath, R., Rodenburg, R. J., Coenen, M. J. H., Janssen, M., Henssen, D., Gilissen, C., Steyaert, W., Paramonov, I., Trimouille, A., Kleefstra, T., Verloes, A., Vissers, L. E. L. M., Nigro, V., Torella, A., and Banfi, S.

Subjects
Male, Proband, Mitochondrial DNA, RNA, Transfer, Leu, Brief Communication, Quadriplegia, Whole Exome Sequencing, Healthcare improvement science Radboud Institute for Health Sciences [Radboudumc 18], Young Adult, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, Intellectual Disability, Exome Sequencing, Genetics research, Intellectual disability, Genetics, medicine, Humans, Genetics (clinical), Exome sequencing, 0303 health sciences, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], business.industry, Neurodevelopmental disorders, 030305 genetics & heredity, Correction, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Translational research, medicine.disease, Heteroplasmy, 3. Good health, MT-TL1, Mutation, Inflammatory diseases Radboud Institute for Health Sciences [Radboudumc 5], Spastic tetraparesis, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Neurological disorders, 030217 neurology & neurosurgery
Abstract

Correction: A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis. Eur J Hum Genet. 2021 Sep;29(9):1470-1471. doi: 10.1038/s41431-021-00937-3. The genetic etiology of intellectual disability remains elusive in almost half of all affected individuals. Within the Solve-RD consortium, systematic re-analysis of whole exome sequencing (WES) data from unresolved cases with (syndromic) intellectual disability (n = 1,472 probands) was performed. This re-analysis included variant calling of mitochondrial DNA (mtDNA) variants, although mtDNA is not specifically targeted in WES. We identified a functionally relevant mtDNA variant in MT-TL1 (NC_012920.1:m.3291T > C; NC_012920.1:n.62T > C), at a heteroplasmy level of 22% in whole blood, in a 23-year-old male with severe intellectual disability, epilepsy, episodic headaches with emesis, spastic tetraparesis, brain abnormalities, and feeding difficulties. Targeted validation in blood and urine supported pathogenicity, with heteroplasmy levels of 23% and 58% in index, and 4% and 17% in mother, respectively. Interestingly, not all phenotypic features observed in the index have been previously linked to this MT-TL1 variant, suggesting either broadening of the m.3291T > C-associated phenotype, or presence of a co-occurring disorder. Hence, our case highlights the importance of underappreciated mtDNA variants identifiable from WES data, especially for cases with atypical mitochondrial phenotypes and their relatives in the maternal line. This work was financially supported by Aspasia grants of the Dutch Research Council (015.014.036 to TK and 015.014.066 to LELMV), the European Research Council (ERC to RH), the Well come Investigator Award (109915/Z/15/Z to RH), the Medical Research Council UK (MR/N025431/1 to RH), the Newton Fund (MR/N027302/1 to RH), the Lily Foundation (RH), and the Evelyn Trust (RH). The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 779257. Sí

Published
2021
Full Text
View/download PDF

26. Monkeypox outbreak in Madrid (Spain): Clinical and virological aspects

Author

Orviz, Eva, primary, Negredo, Anabel, additional, Ayerdi, Oskar, additional, Vázquez, Ana, additional, Muñoz-Gomez, Ana, additional, Monzón, Sara, additional, Clavo, Petunia, additional, Zaballos, Angel, additional, Vera, Mar, additional, Sánchez, Patricia, additional, Cabello, Noemi, additional, Jiménez, Pilar, additional, Pérez-García, Jorge A., additional, Varona, Sarai, additional, del Romero, Jorge, additional, Cuesta, Isabel, additional, Delgado-Iribarren, Alberto, additional, Torres, Montse, additional, Sagastagoitia, Iñigo, additional, Palacios, Gustavo, additional, Estrada, Vicente, additional, Sánchez-Seco, Maria Paz, additional, Ballesteros, Juan, additional, Baza, Begoña, additional, Carrió, Juan Carlos, additional, Chocron, Cynthia, additional, Fedele, Giovanni, additional, García-Amil, Cristina, additional, Herrero, Laura, additional, Homen, Reynaldo, additional, Mariano, Alberto, additional, Martínez-Burgoa, Teresa, additional, Molero, Francisca, additional, Navarro, Maria Luisa, additional, Núñez, Maria José, additional, Perez-Somarriba, Juncal, additional, Puerta, Teresa, additional, Rodríguez-Añover, Javier, additional, Pastrana, Esperanza Pérez, additional, Jiménez, Mercedes, additional, de la Vega, Leticia, additional, Vergas, Jorge, additional, and Zarza, Isabel, additional

Published
2022
Full Text
View/download PDF

27. Changes in a new type of genomic accordion may open the pallets to increased monkeypox transmissibility

Author

Monzón, Sara, primary, Varona, Sarai, additional, Negredo, Anabel, additional, Patiño-Galindo, Juan Angel, additional, Vidal-Freire, Santiago, additional, Zaballos, Angel, additional, Orviz, Eva, additional, Ayerdi, Oskar, additional, Muñoz-García, Ana, additional, Delgado-Iribarren, Alberto, additional, Estrada, Vicente, additional, García, Cristina, additional, Molero, Francisca, additional, Sánchez, Patricia, additional, Torres, Montserrat, additional, Vázquez, Ana, additional, Galán, Juan-Carlos, additional, Torres, Ignacio, additional, Causse del Río, Manuel, additional, Merino, Laura, additional, López, Marcos, additional, Galar, Alicia, additional, Cardeñoso, Laura, additional, Gutiérrez, Almudena, additional, Loras, Cristina, additional, Escribano, Isabel, additional, Alvarez-Argüelles, Marta Elena, additional, del Río, Leticia, additional, Simón, María, additional, Meléndez, MªAngeles, additional, Camacho, Juan, additional, Herrero, Laura, additional, Sancho, Pilar Jiménez, additional, Navarro-Rico, Maria Luisa, additional, Kuhn, Jens H., additional, Sanchez-Lockhart, Mariano, additional, Paola, Nicholas Di, additional, Kugelman, Jeffrey R., additional, Giannetti, Elaina, additional, Guerra, Susana, additional, García-Sastre, Adolfo, additional, Palacios, Gustavo, additional, Cuesta, Isabel, additional, and Sánchez-Seco, Maripaz P., additional

Published
2022
Full Text
View/download PDF

30. Differences in Expression of IQSEC2 Transcript Isoforms in Male and Female Cases with Loss of Function Variants and Neurodevelopmental Disorder

Author

Baladron, Beatriz, primary, Mielu, Lidia M., additional, López-Martín, Estrella, additional, Barrero, Maria J., additional, Lopez, Lidia, additional, Alvarado, Jose I., additional, Monzón, Sara, additional, Varona, Sarai, additional, Cuesta, Isabel, additional, Cazorla, Rosario, additional, Lara, Julián, additional, Iglesias, Gemma, additional, Román, Enriqueta, additional, Ros, Purificación, additional, Gomez-Mariano, Gema, additional, Cubillo, Isabel, additional, Miguel, Esther Hernandez-San, additional, Rivera, Daniel, additional, Alonso, Javier, additional, Bermejo-Sánchez, Eva, additional, Posada, Manuel, additional, and Martínez-Delgado, Beatriz, additional

Published
2022
Full Text
View/download PDF

33. Enhancing SARS-CoV-2 Surveillance through Regular Genomic Sequencing in Spain: The RELECOV Network.

Author

Vázquez-Morón, Sonia, Iglesias-Caballero, María, Lepe, José Antonio, Garcia, Federico, Melón, Santiago, Marimon, José M., García de Viedma, Darío, Folgueira, Maria Dolores, Galán, Juan Carlos, López-Causapé, Carla, Benito-Ruesca, Rafael, Alcoba-Florez, Julia, Gonzalez Candelas, Fernando, Toro, María de, Fajardo, Miguel, Ezpeleta, Carmen, Lázaro, Fernando, Pérez Castro, Sonia, Cuesta, Isabel, and Zaballos, Angel

Subjects
SARS-CoV-2 Omicron variant, SARS-CoV-2 Delta variant, SARS-CoV-2, PUBLIC health surveillance, WHOLE genome sequencing
Abstract

Millions of SARS-CoV-2 whole genome sequences have been generated to date. However, good quality data and adequate surveillance systems are required to contribute to meaningful surveillance in public health. In this context, the network of Spanish laboratories for coronavirus (RELECOV) was created with the main goal of promoting actions to speed up the detection, analyses, and evaluation of SARS-CoV-2 at a national level, partially structured and financed by an ECDC-HERA-Incubator action (ECDC/GRANT/2021/024). A SARS-CoV-2 sequencing quality control assessment (QCA) was developed to evaluate the network's technical capacity. QCA full panel results showed a lower hit rate for lineage assignment compared to that obtained for variants. Genomic data comprising 48,578 viral genomes were studied and evaluated to monitor SARS-CoV-2. The developed network actions showed a 36% increase in sharing viral sequences. In addition, analysis of lineage/sublineage-defining mutations to track the virus showed characteristic mutation profiles for the Delta and Omicron variants. Further, phylogenetic analyses strongly correlated with different variant clusters, obtaining a robust reference tree. The RELECOV network has made it possible to improve and enhance the genomic surveillance of SARS-CoV-2 in Spain. It has provided and evaluated genomic tools for viral genome monitoring and characterization that make it possible to increase knowledge efficiently and quickly, promoting the genomic surveillance of SARS-CoV-2 in Spain. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

35. In Vitro Probiotic Modulation of the Intestinal Microbiota and 2′Fucosyllactose Consumption in Fecal Cultures from Infants at Two Months of Age

Author

Nogacka, Alicja M., primary, Arboleya, Silvia, additional, Nikpoor, Naghmeh, additional, Auger, Jeremie, additional, Salazar, Nuria, additional, Cuesta, Isabel, additional, Alvarez-Buylla, Jorge R., additional, Mantecón, Laura, additional, Solís, Gonzalo, additional, Gueimonde, Miguel, additional, Tompkins, Thomas A., additional, and de los Reyes-Gavilán, Clara G., additional

Published
2022
Full Text
View/download PDF

40. Solving patients with rare diseases through programmatic reanalysis of genome-phenome data

Author

Matalonga, Leslie, Hernández-Ferrer, Carles, DITF-ITHACA, Solve-RD, Verloes, Alain, Vissers, Lisenka, Vitobello, Antonio, Votypka, Pavel, Vyshka, Klea, Zurek, Birte, Baets, Jonathan, Beijer, Danique, Bonne, Gisèle, Cohen, Enzo, DITF-euroNMD, Solve-RD, Cossins, Judith, Evangelista, Teresinha, Ferlini, Alessandra, Hackman, Peter, Hanna, Michael G, Horvath, Rita, Houlden, Henry, Johari, Mridul, Lau, Jarred, Lochmüller, Hanns, DITF-RND, Solve-RD, Macken, William L, Musacchia, Francesco, Nascimento, Andres, Natera-de Benito, Daniel, Nigro, Vincenzo, Piluso, Giulio, Pini, Veronica, Pitceathly, Robert D S, Polavarapu, Kiran, Cruz, Pedro M Rodriguez, Tonda, Raul, Sarkozy, Anna, Savarese, Marco, Selvatici, Rita, Thompson, Rachel, Udd, Bjarne, Van de Vondel, Liedewei, Vandrovcova, Jana, Zaharieva, Irina, Balicza, Peter, Laurie, Steven, Chinnery, Patrick, Dürr, Alexandra, Haack, Tobias, Hengel, Holger, Kamsteeg, Erik-Jan, Kamsteeg, Christoph, Lohmann, Katja, Macaya, Alfons, Marcé-Grau, Anna, Fernandez-Callejo, Marcos, Maver, Ales, Molnar, Judit, Münchau, Alexander, Peterlin, Borut, Riess, Olaf, Schöls, Ludger, Schüle-Freyer, Rebecca, Stevanin, Giovanni, Synofzik, Matthis, Timmerman, Vincent, Picó, Daniel, van de Warrenburg, Bart, van Os, Nienke, Wayand, Melanie, Wilke, Carlo, Haack, Tobias B, Graessner, Holm, Ellwanger, Kornelia, Ossowski, Stephan, Demidov, German, Garcia-Linares, Carles, Sturm, Marc, Schulze-Hentrich, Julia M, Kessler, Christoph, Heutink, Peter, Brunner, Han, Scheffer, Hans, Papakonstantinou, Anastasios, Hoogerbrugge, Nicoline, 't Hoen, Peter A C, Steyaert, Wouter, Sablauskas, Karolis, Te Paske, Iris, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Corvó, Alberto, Brookes, Anthony J, Veal, Colin, Gibson, Spencer, Wadsley, Marc, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Piscia, Davide, Joshi, Ricky, Bettolo, Chiara Marini, Specht, Sabine, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Duffourd, Yannis, Tisserant, Emilie, Diez, Hector, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Bullich, Gemma, Gut, Ivo, Corvo, Alberto, Garcia, Carles, Hernández, Carles, Paramonov, Ida, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hoischen, Alexander, Hanauer, Marc, Olry, Annie, Lagorce, David, Havrylenko, Svitlana, Izem, Katia, Rigour, Fanny, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Allamand, Valérie, Nelson, Isabelle, Yaou, Rabah Ben, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Kremlik, Vlastimil, Parkinson, Helen, Keane, Thomas, Consortia, Solve-RD, Spalding, Dylan, Senf, Alexander, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Reilly, Mary, Muntoni, Francesco, de Jonghe, Peter, Banfi, Sandro, Torella, Annalaura, Cuesta, Isabel, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Peters, Sophia, Oliveira, Carla, Pelaez, Jose Garcia, Matos, Ana Rita, José, Celina São, Ferreira, Marta, Gullo, Irene, Fernandes, Susana, Garrido, Luzia, Ferreira, Pedro, Carneiro, Fátima, Swertz, Morris A, Johansson, Lennart, van der Vries, Gerben, Neerincx, Pieter B, group, Solve-RD SNV-indel working, Denommé-Pichon, Anne-Sophie, Roelofs-Prins, Dieuwke, Köhler, Sebastian, Metcalfe, Alison, Rooryck, Caroline, Trimouille, Aurelien, Castello, Raffaele, Morleo, Manuela, Varavallo, Alessandra, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, de la Rosa, F Javier Alonso García, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Benetti, Elisa, Molnar, Maria Judit, Gilissen, Christian, Herzog, Rebecca, Pauly, Martje, Osorio, Andres Nascimiento, de Benito, Daniel Natera, Beeson, David, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Li, Shuang, Prasanth, Sivakumar, Robinson, Peter, van der Velde, Joeri K, de Voer, Richarda M, Evans, Gareth, Sommer, Anna Katharina, Töpf, Ana, Paske, Iris Te, Tischkowitz, Marc, Casari, Giorgio, Ciolfi, Andrea, Dallapiccola, Bruno, de Boer, Elke, Vissers, Lisenka E L M, Hammarsjö, Anna, Havlovicova, Marketa, Hugon, Anne, de Voer, Richarda, Kleefstra, Tjitske, Lindstrand, Anna, López-Martín, Estrella, Nigro, Vicenzo, Nordgren, Ann, Pettersson, Maria, Pinelli, Michele, Pizzi, Simone, DITF-GENTURIS, Solve-RD, Posada, Manuel, Ryba, Lukas, Schwarz, Martin, Trimouille, Aurélien, Solve RD SNV Indel Working Grp, Solve RD DITF GENTURIS, Solve RD DITF ITHACA, Solve RD DITF-euroNMD, Solve RD DITF RND, Solve RD Consortia, Matalonga, L., Hernandez-Ferrer, C., Piscia, D., Cohen, E., Cuesta, I., Danis, D., Denomme-Pichon, A. -S., Duffourd, Y., Gilissen, C., Johari, M., Laurie, S., Li, S., Nelson, I., Peters, S., Paramonov, I., Prasanth, S., Robinson, P., Sablauskas, K., Savarese, M., Steyaert, W., van der Velde, J. K., Vitobello, A., Schule, R., Synofzik, M., Topf, A., Vissers, L. E. L. M., de Voer, R., Aretz, S., Capella, G., de Voer, R. M., Evans, G., Pelaez, J. G., Holinski-Feder, E., Hoogerbrugge, N., Laner, A., Oliveira, C., Rump, A., Schrock, E., Sommer, A. K., Steinke-Lange, V., Paske, I., Tischkowitz, M., Valle, L., Banka, S., Benetti, E., Casari, G., Ciolfi, A., Clayton-Smith, J., Dallapiccola, B., de Boer, E., Ellwanger, K., Faivre, L., Graessner, H., Haack, T. B., Hammarsjo, A., Havlovicova, M., Hoischen, A., Hugon, A., Jackson, A., Kleefstra, T., Lindstrand, A., Lopez-Martin, E., Macek, M., Morleo, M., Nigro, V., Nordgren, A., Pettersson, M., Pinelli, M., Pizzi, S., Posada, M., Radio, F. C., Renieri, A., Rooryck, C., Ryba, L., Schwarz, M., Tartaglia, M., Thauvin, C., Torella, A., Trimouille, A., Verloes, A., Vissers, L., Votypka, P., Vyshka, K., Zurek, B., Baets, J., Beijer, D., Bonne, G., Cossins, J., Evangelista, T., Ferlini, A., Hackman, P., Hanna, M. G., Horvath, R., Houlden, H., Lau, J., Lochmuller, H., Macken, W. L., Musacchia, F., Nascimento, A., Natera-de Benito, D., Piluso, G., Pini, V., Pitceathly, R. D. S., Polavarapu, K., Cruz, P. M. R., Sarkozy, A., Selvatici, R., Thompson, R., Udd, B., Van de Vondel, L., Vandrovcova, J., Zaharieva, I., Balicza, P., Chinnery, P., Durr, A., Haack, T., Hengel, H., Kamsteeg, E. -J., Kamsteeg, C., Lohmann, K., Macaya, A., Marce-Grau, A., Maver, A., Molnar, J., Munchau, A., Peterlin, B., Riess, O., Schols, L., Schule-Freyer, R., Stevanin, G., Timmerman, V., van de Warrenburg, B., van Os, N., Wayand, M., Wilke, C., Tonda, R., Fernandez-Callejo, M., Pico, D., Garcia-Linares, C., Papakonstantinou, A., Corvo, A., Joshi, R., Diez, H., Gut, I., Beltran, S., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Kessler, C., Heutink, P., Brunner, H., Scheffer, H., 't Hoen, P. A. C., te Paske, I., Janssen, E., Steehouwer, M., Yaldiz, B., Brookes, A. J., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Specht, S., Alexander, E., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Gut, I. G., Bullich, G., Garcia, C., Hernandez, C., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Olry, A., Lagorce, D., Havrylenko, S., Izem, K., Rigour, F., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Allamand, V., Yaou, R. B., Metay, C., Eymard, B., Atalaia, A., Stojkovic, T., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Kremlik, V., Parkinson, H., Keane, T., Spalding, D., Senf, A., Robert, G., Costa, A., Patch, C., Hanna, M., Reilly, M., Muntoni, F., de Jonghe, P., Banfi, S., Rossi, R., Neri, M., Spier, I., Matos, A. R., Jose, C. S., Ferreira, M., Gullo, I., Fernandes, S., Garrido, L., Ferreira, P., Carneiro, F., Swertz, M. A., Johansson, L., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Castello, R., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., de la Rosa, F. J. A. G., Molnar, M. J., Herzog, R., Pauly, M., Osorio, A. N., de Benito, D. N., Beeson, D., Unión Europea. Comisión Europea. H2020, Instituto de Salud Carlos III, Ministerio de Economía, Industria y Competitividad (España), Ministerio de Ciencia e Innovación. Centro de Excelencia Severo Ochoa (España), Government of Catalonia (España), Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Instituto Nacional de Bioinformatica (España), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA Klinische Genetica (5), Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), Instituto de Salud Carlos III [Madrid] (ISC), Radboud University Medical Center [Nijmegen], Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Equipe GAD (LNC - U1231), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Barcelona Institute of Science and Technology (BIST), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Folkhälsan Research Center, Faculty of Medecine [Helsinki], University of Helsinki-University of Helsinki, Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Myologie, University of Helsinki, Department of Medical and Clinical Genetics, Medicum, and Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

Subjects
Genetic testing, Computer science, genetics [Rare Diseases], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], EXOME, MEDICAL GENETICS, Diseases, Disease, VARIANTS, Genome informatics, Genomic analysis, Diseases, Genetic testing, Genome informatics, Genomic analysis, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Exome, Genetics (clinical), Exome sequencing, 0303 health sciences, Application programming interface, methods [Genomics], 030305 genetics & heredity, 1184 Genetics, developmental biology, physiology, Genomics, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], 3. Good health, Pedigree, diagnosis [Rare Diseases], Chemistry, Medical genetics, medicine.medical_specialty, methods [Genetic Testing], MEDLINE, Socio-culturale, Phenome, AMERICAN-COLLEGE, INHERITANCE, Sensitivity and Specificity, Article, standards [Genetic Testing], 03 medical and health sciences, Rare Diseases, [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Genetics, medicine, Humans, ddc:610, Genetic Testing, Biology, 030304 developmental biology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Data science, Workflow, 3111 Biomedicine, standards [Genomics], Human medicine, Software
Abstract

Correction to: Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. Eur J Hum Genet. 2021 Sep;29(9):1466-1469. doi: 10.1038/s41431-021-00934-6. PMID: 34393220 Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. Data were analysed using the RD‐Connect Genome‐Phenome Analysis Platform, which received funding from EU projects RD‐Connect, Solve-RD and EJP-RD (grant numbers FP7 305444, H2020 779257, H2020 825575), Instituto de Salud Carlos III (grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática, INB) and ELIXIR Implementation Studies. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme/Generalitat de Catalunya. We also acknowledge the support of the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement and the Co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program. Sí

Published
2021
Full Text
View/download PDF

41. Influence of 2′-Fucosyllactose on the Microbiota Composition and Metabolic Activity of Fecal Cultures from Breastfed and Formula-Fed Infants at Two Months of Age

Author

Nogacka, Alicja M., primary, Arboleya, Silvia, additional, Nikpoor, Naghmeh, additional, Auger, Jeremie, additional, Salazar, Nuria, additional, Cuesta, Isabel, additional, Mantecón, Laura, additional, Solís, Gonzalo, additional, Gueimonde, Miguel, additional, Tompkins, Thomas A., additional, and de los Reyes-Gavilán, Clara G., additional

Published
2021
Full Text
View/download PDF

43. Exome reanalysis and proteomic profiling identified TRIP4 as a novel cause of cerebellar hypoplasia and spinal muscular atrophy (PCH1)

Author

Töpf, Ana, Pyle, Angela, Griffin, Helen, Matalonga, Leslie, Schon, Katherine, Sickmann, Albert, Schara–Schmidt, Ulrike, Hentschel, Andreas, Chinnery, Patrick F., Kölbel, Heike, Roos, Andreas, Horvath, Rita, Cohen, Enzo, Cuesta, Isabel, Danis, Daniel, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Gilissen, Christian, Johari, Mridul, Laurie, Steven, Li, Shuang, Nelson, Isabelle, Paramonov, Ida, Peters, Sophia, Prasanth, Sivakumar, Robinson, Peter, Sablauskas, Karolis, Savarese, Marco, Steyaert, Wouter, Van Der Velde, Joeri K., Vitobello, Antonio, Baets, Jonathan, Beijer, Danique, Bonne, Gisèle, Cossins, Judith, Evangelista, Teresinha, Ferlini, Alessandra, Hackman, Peter, Hanna, Michael G., Houlden, Henry, Lau, Jarred, Lochmüller, Hanns, Macken, William L., Musacchia, Francesco, Nascimento, Andres, Natera-De Benito, Daniel, Nigro, Vincenzo, Piluso, Giulio, Pini, Veronica, Pitceathly, Robert D. S., Polavarapu, Kiran, Cruz, Pedro M. Rodriguez, Sarkozy, Anna, Selvatici, Rita, Thompson, Rachel, Torella, Annalaura, Udd, Bjarne, Van De Vondel, Liedewei, Vandrovcova, Jana, Zaharieva, Irina, Schon, Katherine [0000-0001-8054-8954], Horvath, Rita [0000-0002-9841-170X], Apollo - University of Cambridge Repository, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Barcelona Institute of Science and Technology (BIST), University of Cambridge [UK] (CAM), Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., University of Aberdeen, Ruhr-Universität Bochum [Bochum], University Children's Hospital of Essen [Essen, Germany], Enzo Cohen, Isabel Cuesta, Daniel Danis, Anne-Sophie Denommé-Pichon, Yannis Duffourd, Christian Gilissen, Mridul Johari, Steven Laurie, Shuang Li, Isabelle Nelson, Ida Paramonov, Sophia Peters, Sivakumar Prasanth, Peter Robinson, Karolis Sablauskas, Marco Savarese, Wouter Steyaert, Joeri K van der Velde, Antonio Vitobello, Jonathan Baets, Danique Beijer, Gisèle Bonne, Judith Cossins, Teresinha Evangelista, Alessandra Ferlini, Peter Hackman, Michael G Hanna, Henry Houlden, Jarred Lau, Hanns Lochmüller, William L Macken, Francesco Musacchia, Andres Nascimento, Daniel Natera-de Benito, Vincenzo Nigro, Giulio Piluso, Veronica Pini, Robert D S Pitceathly, Kiran Polavarapu, Pedro M Rodriguez Cruz, Anna Sarkozy, Rita Selvatici, Rachel Thompson, Annalaura Torella, Bjarne Udd, Liedewei Van de Vondel, Jana Vandrovcova, Irina Zaharieva, Töpf, Ana, Pyle, Angela, Griffin, Helen, Matalonga, Leslie, Schon, Katherine, Sickmann, Albert, Schara-Schmidt, Ulrike, Hentschel, Andrea, Chinnery, Patrick F, Kölbel, Heike, Roos, Andrea, Horvath, Rita, Nigro, Vincenzo, Torella, Annalaura, and Piluso, Giulio

Subjects
0301 basic medicine, Male, Proteome, 45/41, Developmental Disabilities, Medizin, 45/22, Biology, Bioinformatics, Nervous System Malformations, Brief Communication, 82/80, Muscular Atrophy, Spinal, 03 medical and health sciences, 0302 clinical medicine, Cerebellum, 38/23, Genetics research, Genetics, medicine, [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Humans, Exome, Genetic Testing, Gene, Cerebellar hypoplasia, Genetics (clinical), Exome sequencing, Proteomic Profile, Proteomic Profiling, 82/58, 631/208/514/2254, brief-communication, 692/308/2056, Infant, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Spinal muscular atrophy, medicine.disease, 3. Good health, 030104 developmental biology, Congenital muscular dystrophy, Next-generation sequencing, 030217 neurology & neurosurgery, Transcription Factors
Abstract

TRIP4 is one of the subunits of the transcriptional coregulator ASC-1, a ribonucleoprotein complex that participates in transcriptional coactivation and RNA processing events. Recessive variants in the TRIP4 gene have been associated with spinal muscular atrophy with bone fractures as well as a severe form of congenital muscular dystrophy. Here we present the diagnostic journey of a patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures. Initial exome sequencing analysis revealed no candidate variants. Reanalysis of the exome data by inclusion in the Solve-RD project resulted in the identification of a homozygous stop-gain variant in the TRIP4 gene, previously reported as disease-causing. This highlights the importance of analysis reiteration and improved and updated bioinformatic pipelines. Proteomic profile of the patient's fibroblasts showed altered RNA-processing and impaired exosome activity supporting the pathogenicity of the detected variant. In addition, we identified a novel genetic form of PCH1, further strengthening the link of this characteristic phenotype with altered RNA metabolism. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. Several authors of this study are members of the European Reference Network for Neuromuscular disease, Project ID No 739543. This study was supported by the AFM (grant 21644 to AR), the framework of the NME-GPS project by the European Regional Development Fund (AR/US/AS), the support by the Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen, the Regierende Bürgermeister von Berlin-inkl. Wissenschaft und Forschung, and the Bundesministerium für Bildung und Forschung (AH and AS), the European Research Council (RH), the Wellcome Investigator Award (109915/Z/15/Z to RH), the Medical Research Council UK (MR/N025431/1 to RH), the Newton Fund (MR/N027302/1 to RH), the Lily Foundation (RH) and the Evelyn Trust (RH). This research was supported by an MRC strategic award to establish an International Centre for Genomic Medicine in Neuromuscular Diseases (ICGNMD) MR/S005021/1 and the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014). The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care

Published
2020
Full Text
View/download PDF

44. Molecular Characterization and Antimicrobial Susceptibilities of Nocardia Species Isolated from the Soil

Author

Carrasco, Gema, Monzón, Sara, Segundo, María San, García, Enrique, Garrido, Noelia, Medina-Pascual, María J., Villalón, Pilar, Ramírez, Ana, Jiménez, Pilar, Cuesta, Isabel, and Valdezate, Sylvia

Subjects
MLSA, gyrB, bacteria, antimicrobial resistance, Nocardia spp, bacterial infections and mycoses, potential new species/subspecies N. venezuelensis, WGS, Nocardia cyriacigeorgica, soil, nocardiosis
Abstract

Nocardia species, one of the most predominant Actinobacteria of the soil microbiota, cause infection in humans following traumatic inoculation or inhalation. The identification, typing, phylogenetic relationship and antimicrobial susceptibilities of 38 soil Nocardia strains from Lara State, Venezuela, were studied by 16S rRNA and gyrB (subunit B of topoisomerase II) genes, multilocus sequence analysis (MLSA), whole-genome sequencing (WGS), and microdilution. The results were compared with those for human strains. Just seven Nocardia species with one or two strains each, except for Nocardia cyriacigeorgica with 29, were identified. MLSA confirmed the species assignments made by 16S rRNA and gyrB analyses (89.5% and 71.0% respectively), and grouped each soil strain with its corresponding reference and clinical strains, except for 19 N. cyriacigeorgica strains found at five locations which grouped into a soil-only cluster. The soil strains of N. cyriacigeorgica showed fewer gyrB haplotypes than the examined human strains (13 vs. 17) but did show a larger number of gyrB SNPs (212 vs. 77). Their susceptibilities to antimicrobials were similar except for beta-lactams, fluoroquinolones, minocycline, and clarithromycin, with the soil strains more susceptible to the first three (p &le, 0.05). WGS was performed on four strains belonging to the soil-only cluster and on two outside it, and the results compared with public N. cyriacigeorgica genomes. The average nucleotide/amino acid identity, in silico genome-to-genome hybridization similarity, and the difference in the genomic GC content, suggest that some strains of the soil-only cluster may belong to a novel subspecies or even a new species (proposed name Nocardia venezuelensis).

Published
2020
Full Text
View/download PDF

48. A Founder Effect Led Early SARS-CoV-2 Transmission in Spain

Author

Díez-Fuertes, Francisco, primary, Iglesias-Caballero, María, additional, García-Pérez, Javier, additional, Monzón, Sara, additional, Jiménez, Pilar, additional, Varona, Sarai, additional, Cuesta, Isabel, additional, Zaballos, Ángel, additional, Jiménez, Mercedes, additional, Checa, Laura, additional, Pozo, Francisco, additional, Pérez-Olmeda, Mayte, additional, Thomson, Michael M., additional, Alcamí, José, additional, and Casas, Inmaculada, additional

Published
2021
Full Text
View/download PDF

50. De novo small deletion affecting transcription start site of short isoform ofAUTS2gene in a patient with syndromic neurodevelopmental defects

Author

Martinez‐Delgado, Beatriz, primary, Lopez‐Martin, Estrella, additional, Lara‐Herguedas, Julián, additional, Monzon, Sara, additional, Cuesta, Isabel, additional, Juliá, Miguel, additional, Aquino, Virginia, additional, Rodriguez‐Martin, Carlos, additional, Damian, Alejandra, additional, Gonzalo, Irene, additional, Gomez‐Mariano, Gema, additional, Baladron, Beatriz, additional, Cazorla, Rosario, additional, Iglesias, Gema, additional, Roman, Enriqueta, additional, Ros, Purificacion, additional, Tutor, Pablo, additional, Mellor, Susana, additional, Jimenez, Carlos, additional, Cabrejas, Maria Jose, additional, Gonzalez‐Vioque, Emiliano, additional, Alonso, Javier, additional, Bermejo‐Sánchez, Eva, additional, and Posada, Manuel, additional

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results