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1. DOP56 Fibrosis-related transcriptome unveils a distinctive matrix remodelling pattern in penetrating but not in stricturing ileal Crohn's Disease

Author: Tavares de Sousa, H, primary, Ferreira, M, additional, Gullo, I, additional, Rocha, A M, additional, Oliveira, C, additional, Carneiro, F, additional, and Magro, F, additional
Published: 2024
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2. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author: Denomme-Pichon A. -S., Bruel A. -L., Duffourd Y., Safraou H., Thauvin-Robinet C., Tran Mau-Them F., Philippe C., Vitobello A., Jean-Marcais N., Moutton S., Thevenon J., Faivre L., Matalonga L., de Boer E., Gilissen C., Hoischen A., Kleefstra T., Pfundt R., de Vries B. B. A., Willemsen M. H., Vissers L. E. L. M., Jackson A., Banka S., Clayton-Smith J., Benetti E., Fallerini C., Renieri A., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Ellwanger K., Graessner H., Haack T. B., Zurek B., Havlovicova M., Macek M., Ryba L., Schwarz M., Votypka P., Lopez-Martin E., Posada M., Mencarelli M. A., Rooryck C., Trimouille A., Verloes A., Abbott K. M., Kerstjens M., Martin E. L., Maystadt I., Morleo M., Nigro V., Pinelli M., Riess O., Agathe J. -M. D. S., Santen G. W. E., Thauvin C., Torella A., Vissers L., Zguro K., Boer E. D., Cohen E., Danis D., Gao F., Horvath R., Johari M., Johanson L., Li S., Morsy H., Nelson I., Paramonov I., te Paske I. B. A. W., Robinson P., Savarese M., Steyaert W., Topf A., van der Velde J. K., Vandrovcova J., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Schule R., Xu J., Kessler C., Wayand M., Synofzik M., Wilke C., Traschutz A., Schols L., Hengel H., Lerche H., Kegele J., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., 't Hoen P. A. C., Sablauskas K., de Voer R. M., Kamsteeg E. -J., van de Warrenburg B., van Os N., Paske I. T., Janssen E., Steehouwer M., Yaldiz B., Brookes A. J., Veal C., Gibson S., Maddi V., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Straub V., Bettolo C. M., Manera J. D., Hambleton S., Engelhardt K., Alexander E., Peyron C., Pelissier A., Beltran S., Gut I. G., Laurie S., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Fernandez-Callejo M., Hernandez C., Pico D., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Lagorce D., Hongnat O., Chahdil M., Lebreton E., Stevanin G., Durr A., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Ben Yaou R., Metay C., Eymard B., Atalaia A., Stojkovic T., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Liskova P., Dolezalova P., Parkinson H., Keane T., Freeberg M., Thomas C., Spalding D., Robert G., Costa A., Patch C., Hanna M., Houlden H., Reilly M., Efthymiou S., Cali E., Magrinelli F., Sisodiya S. M., Rohrer J., Muntoni F., Zaharieva I., Sarkozy A., Timmerman V., Baets J., de Vries G., De Winter J., Beijer D., de Jonghe P., Van de Vondel L., De Ridder W., Weckhuysen S., Mutarelli M., Varavallo A., Banfi S., Musacchia F., Piluso G., Ferlini A., Selvatici R., Gualandi F., Bigoni S., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., 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., Ruvolo D., Kerstjens Frederikse W. S., Zonneveld-Huijssoon E., Roelofs-Prins D., van Gijn M., Kohler S., Metcalfe A., Drunat S., Heron D., Mignot C., Keren B., Lacombe D., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Cilio M. -R., Carpancea E., Depondt C., Lederer D., Sznajer Y., Duerinckx S., Mary S., Macaya A., Cazurro-Gutierrez A., Perez-Duenas B., Munell F., Jarava C. F., Maso L. B., Marce-Grau A., Colobran R., Hackman P., Udd B., Hemelsoet D., Dermaut B., Schuermans N., Poppe B., Verdin H., Osorio A. N., Depienne C., Roos A., Cordts I., Deschauer M., Striano P., Zara F., Riva A., Iacomino M., Uva P., Scala M., Scudieri P., Basak A. N., Claeys K., Boztug K., Haimel M., W. E G., Ruivenkamp C. A. L., Natera de Benito D., Thompson R., Polavarapu K., Grimbacher B., Zaganas I., Kokosali E., Lambros M., Evangeliou A., Spilioti M., Kapaki E., Bourbouli M., Balicza P., Molnar M. J., De la Paz M. P., Sanchez E. B., Delgado B. M., Alonso Garcia de la Rosa F. J., Schrock E., Rump A., Mei D., Vetro A., Balestrini S., Guerrini R., Chinnery P. F., Ratnaike T., Schon K., Maver A., Peterlin B., Munchau A., Lohmann K., Herzog R., Pauly M., May P., Beeson D., Cossins J., Furini S., Afenjar A., Goldenberg A., Masurel A., Phan A., Dieux-Coeslier A., Fargeot A., Guerrot A. -M., Toutain A., Molin A., Sorlin A., Putoux A., Jouret B., Laudier B., Demeer B., Doray B., Bonniaud B., Isidor B., Gilbert-Dussardier B., Leheup B., Reversade B., Paul C., Vincent-Delorme C., Neiva C., Poirsier C., Quelin C., Chiaverini C., Coubes C., Francannet C., Colson C., Desplantes C., Wells C., Goizet C., Sanlaville D., Amram D., Lehalle D., Genevieve D., Gaillard D., Zivi E., Sarrazin E., Steichen E., Schaefer E., Lacaze E., Jacquemin E., Bongers E., Kilic E., Colin E., Giuliano F., Prieur F., Laffargue F., Morice-Picard F., Petit F., Cartault F., Feillet F., Baujat G., Morin G., Diene G., Journel H., Perthus I., Lespinasse J., Alessandri J. -L., Amiel J., Martinovic J., Delanne J., Albuisson J., Lambert L., Perrin L., Ousager L. B., Van Maldergem L., Pinson L., Ruaud L., Samimi M., Bournez M., Bonnet-Dupeyron M. N., Vincent M., Jacquemont M. -L., Cordier-Alex M. -P., Gerard-Blanluet M., Willems M., Spodenkiewicz M., Doco-Fenzy M., Rossi M., Renaud M., Fradin M., Mathieu M., Holder-Espinasse M. H., Houcinat N., Hanna N., Leperrier N., Chassaing N., Philip N., Boute O., Van Kien P. K., Parent P., Bitoun P., Sarda P., Vabres P., Jouk P. -S., Touraine R., El Chehadeh S., Whalen S., Marlin S., Passemard S., Grotto S., Bellanger S. A., Blesson S., Nambot S., Naudion S., Lyonnet S., Odent S., Attie-Bitach T., Busa T., Drouin-Garraud V., Layet V., Bizaoui V., Cusin V., Capri Y., Alembik Y., Unión Europea. Comisión Europea. H2020, Unión Europea. Comisión Europea. 7 Programa Marco, Instituto de Salud Carlos III, Instituto Nacional de Bioinformatica (España), Ministry of Health (República Checa), Ministry of Education, Youth and Sports (República Checa), Denomme-Pichon, A. -S., Bruel, A. -L., Duffourd, Y., Safraou, H., Thauvin-Robinet, C., Tran Mau-Them, F., Philippe, C., Vitobello, A., Jean-Marcais, N., Moutton, S., Thevenon, J., Faivre, L., Matalonga, L., de Boer, E., Gilissen, C., Hoischen, A., Kleefstra, T., Pfundt, R., de Vries, B. B. A., Willemsen, M. H., Vissers, L. E. L. M., Jackson, A., Banka, S., Clayton-Smith, J., Benetti, E., Fallerini, C., Renieri, A., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Ellwanger, K., Graessner, H., Haack, T. B., Zurek, B., Havlovicova, M., Macek, M., Ryba, L., Schwarz, M., Votypka, P., Lopez-Martin, E., Posada, M., Mencarelli, M. A., Rooryck, C., Trimouille, A., Verloes, A., Abbott, K. M., Kerstjens, M., Martin, E. L., Maystadt, I., Morleo, M., Nigro, V., Pinelli, M., Riess, O., Agathe, J. -M. D. S., Santen, G. W. E., Thauvin, C., Torella, A., Vissers, L., Zguro, K., Boer, E. D., Cohen, E., Danis, D., Gao, F., Horvath, R., Johari, M., Johanson, L., Li, S., Morsy, H., Nelson, I., Paramonov, I., te Paske, I. B. A. W., Robinson, P., Savarese, M., Steyaert, W., Topf, A., van der Velde, J. K., Vandrovcova, J., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Schule, R., Xu, J., Kessler, C., Wayand, M., Synofzik, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Lerche, H., Kegele, J., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., 't Hoen, P. A. C., Sablauskas, K., de Voer, R. M., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., Paske, I. T., Janssen, E., Steehouwer, M., Yaldiz, B., Brookes, A. J., Veal, C., Gibson, S., Maddi, V., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Manera, J. D., Hambleton, S., Engelhardt, K., Alexander, E., Peyron, C., Pelissier, A., Beltran, S., Gut, I. G., Laurie, S., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Fernandez-Callejo, M., Hernandez, C., Pico, D., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Lagorce, D., Hongnat, O., Chahdil, M., Lebreton, E., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Ben Yaou, R., Metay, C., Eymard, B., Atalaia, A., Stojkovic, T., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Liskova, P., Dolezalova, P., Parkinson, H., Keane, T., Freeberg, M., Thomas, C., Spalding, D., Robert, G., Costa, A., Patch, C., Hanna, M., Houlden, H., Reilly, M., Efthymiou, S., Cali, E., Magrinelli, F., Sisodiya, S. M., Rohrer, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., de Vries, G., De Winter, J., Beijer, D., de Jonghe, P., Van de Vondel, L., De Ridder, W., Weckhuysen, S., Mutarelli, M., Varavallo, A., Banfi, S., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Gualandi, F., Bigoni, S., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., 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., Ruvolo, D., Kerstjens Frederikse, W. S., Zonneveld-Huijssoon, E., Roelofs-Prins, D., van Gijn, M., Kohler, S., Metcalfe, A., Drunat, S., Heron, D., Mignot, C., Keren, B., Lacombe, D., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Cilio, M. -R., Carpancea, E., Depondt, C., Lederer, D., Sznajer, Y., Duerinckx, S., Mary, S., Macaya, A., Cazurro-Gutierrez, A., Perez-Duenas, B., Munell, F., Jarava, C. F., Maso, L. B., Marce-Grau, A., Colobran, R., Hackman, P., Udd, B., Hemelsoet, D., Dermaut, B., Schuermans, N., Poppe, B., Verdin, H., Osorio, A. N., Depienne, C., Roos, A., Cordts, I., Deschauer, M., Striano, P., Zara, F., Riva, A., Iacomino, M., Uva, P., Scala, M., Scudieri, P., Basak, A. N., Claeys, K., Boztug, K., Haimel, M., W. E, G., Ruivenkamp, C. A. L., Natera de Benito, D., Thompson, R., Polavarapu, K., Grimbacher, B., Zaganas, I., Kokosali, E., Lambros, M., Evangeliou, A., Spilioti, M., Kapaki, E., Bourbouli, M., Balicza, P., Molnar, M. J., De la Paz, M. P., Sanchez, E. B., Delgado, B. M., Alonso Garcia de la Rosa, F. J., Schrock, E., Rump, A., Mei, D., Vetro, A., Balestrini, S., Guerrini, R., Chinnery, P. F., Ratnaike, T., Schon, K., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., May, P., Beeson, D., Cossins, J., Furini, S., Afenjar, A., Goldenberg, A., Masurel, A., Phan, A., Dieux-Coeslier, A., Fargeot, A., Guerrot, A. -M., Toutain, A., Molin, A., Sorlin, A., Putoux, A., Jouret, B., Laudier, B., Demeer, B., Doray, B., Bonniaud, B., Isidor, B., Gilbert-Dussardier, B., Leheup, B., Reversade, B., Paul, C., Vincent-Delorme, C., Neiva, C., Poirsier, C., Quelin, C., Chiaverini, C., Coubes, C., Francannet, C., Colson, C., Desplantes, C., Wells, C., Goizet, C., Sanlaville, D., Amram, D., Lehalle, D., Genevieve, D., Gaillard, D., Zivi, E., Sarrazin, E., Steichen, E., Schaefer, E., Lacaze, E., Jacquemin, E., Bongers, E., Kilic, E., Colin, E., Giuliano, F., Prieur, F., Laffargue, F., Morice-Picard, F., Petit, F., Cartault, F., Feillet, F., Baujat, G., Morin, G., Diene, G., Journel, H., Perthus, I., Lespinasse, J., Alessandri, J. -L., Amiel, J., Martinovic, J., Delanne, J., Albuisson, J., Lambert, L., Perrin, L., Ousager, L. B., Van Maldergem, L., Pinson, L., Ruaud, L., Samimi, M., Bournez, M., Bonnet-Dupeyron, M. N., Vincent, M., Jacquemont, M. -L., Cordier-Alex, M. -P., Gerard-Blanluet, M., Willems, M., Spodenkiewicz, M., Doco-Fenzy, M., Rossi, M., Renaud, M., Fradin, M., Mathieu, M., Holder-Espinasse, M. H., Houcinat, N., Hanna, N., Leperrier, N., Chassaing, N., Philip, N., Boute, O., Van Kien, P. K., Parent, P., Bitoun, P., Sarda, P., Vabres, P., Jouk, P. -S., Touraine, R., El Chehadeh, S., Whalen, S., Marlin, S., Passemard, S., Grotto, S., Bellanger, S. A., Blesson, S., Nambot, S., Naudion, S., Lyonnet, S., Odent, S., Attie-Bitach, T., Busa, T., Drouin-Garraud, V., Layet, V., Bizaoui, V., Cusin, V., Capri, Y., Alembik, Y., and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]
Subjects: Exome reanalysis, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Developmental disorder, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology and Life Sciences, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], ClinVar, Rare diseases, All institutes and research themes of the Radboud University Medical Center, Medicine and Health Sciences, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Multidisciplinary, general & others [D99] [Human health sciences], Exome reanalysi, Genetics (clinical)
Abstract: Purpose: Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods: Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results: We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion: The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 779257. Data were analyzed using the RD-Connect Genome-Phenome Analysis Platform, which received funding from the EU projects RD-Connect, Solve-RD, and European Joint Programme on Rare Diseases (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), and ELIXIR Implementation Studies. The collaborations in this study were facilitated by the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies, one of the 24 European Reference Networks approved by the European Reference Network Board of Member States, cofunded by the European Commission. This project was supported by the Czech Ministry of Health (number 00064203) and by the Czech Ministry of Education, Youth and Sports (number - LM2018132) to M.M. Sí
Published: 2023

3. Un ambiente con decorazione in I stile pompeiano dal sito di Monte Iato (PA, Sicilia)

Author: Böhmer, Maria, Bridel, Caroline, Gullo, Ilaria, Böhmer, M ( Maria ), Bridel, C ( Caroline ), Gullo, I ( Ilaria ), Bechi, Eleonora, Böhmer, Maria, Bridel, Caroline, Gullo, Ilaria, Böhmer, M ( Maria ), Bridel, C ( Caroline ), Gullo, I ( Ilaria ), and Bechi, Eleonora
Published: 2023

4. Gastric cancer genetic predisposition and clinical presentations: Established heritable causes and potential candidate genes

Author: Garcia-Pelaez, J., Barbosa-Matos, Rita, Jose, Celina Sao, Sousa, S., Gullo, I., Hoogerbrugge, N., Carneiro, F., Oliveira, Carla, Garcia-Pelaez, J., Barbosa-Matos, Rita, Jose, Celina Sao, Sousa, S., Gullo, I., Hoogerbrugge, N., Carneiro, F., and Oliveira, Carla
Abstract: Item does not contain fulltext
Published: 2022

5. Correction: Solving unsolved rare neurological diseases—a Solve-RD viewpoint (European Journal of Human Genetics, (2021), 29, 9, (1332-1336), 10.1038/s41431-021-00901-1)

Author: Schule R., Timmann D., Erasmus C. E., Reichbauer J., Wayand M., Baets J., Balicza P., Chinnery P., Durr A., Haack T., Hengel H., Horvath R., Houlden 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., Stevanin G., Synofzik M., Timmerman V., van de Warrenburg B., van Os N., Vandrovcova J., Wilke C., Bevot A., Zuchner S., Beltran S., Laurie S., Matalonga L., Graessner H., Zurek B., Ellwanger K., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., Hoischen A., 't Hoen P. A. C., Vissers L. E. L. M., Gilissen C., Steyaert W., Sablauskas K., de Voer R. M., Janssen E., de Boer E., Steehouwer M., Yaldiz B., Kleefstra T., Brookes A. J., Veal C., Gibson S., Wadsley M., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Topf A., Straub V., Bettolo C. M., Specht S., Clayton-Smith J., Banka S., Alexander E., Jackson A., Faivre L., Thauvin C., Vitobello A., Denomme-Pichon A. -S., Duffourd Y., Tisserant E., Bruel A. -L., Peyron C., Pelissier A., Gut I. G., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Garcia C., Fernandez-Callejo M., Hernandez C., Pico D., Paramonov I., Lochmuller H., 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., Bonne G., Evangelista T., Allamand V., Nelson I., Yaou R. B., Metay C., Eymard B., Cohen E., Atalaia A., Stojkovic T., Macek M., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Havlovicova M., Kremlik V., Parkinson H., Keane T., Spalding D., Senf A., Robinson P., Danis D., Robert G., Costa A., Patch C., Hanna M., Reilly M., Muntoni F., Zaharieva I., Sarkozy A., de Jonghe P., Nigro V., Banfi S., Torella A., Musacchia F., Piluso G., Ferlini A., Selvatici R., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., 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 Velde J. K., van der Vries G., Neerincx P. B., Roelofs-Prins D., Kohler S., Metcalfe A., Verloes A., Drunat S., Rooryck C., Trimouille A., Castello R., Morleo M., Pinelli M., Varavallo A., De la Paz M. P., Sanchez E. B., Martin E. L., Delgado B. M., de la Rosa F. J. A. G., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Renieri A., Benetti E., Molnar M. J., Herzog R., Pauly M., Osorio A. N., de Benito D. N., Thompson R., Polavarapu K., Beeson D., Cossins J., Cruz P. M. R., Hackman P., Johari M., Savarese M., Udd B., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Schrock E., Rump A., Schule, R., Timmann, D., Erasmus, C. E., Reichbauer, J., Wayand, M., Baets, J., Balicza, P., Chinnery, P., Durr, A., Haack, T., Hengel, H., Horvath, R., Houlden, 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., Stevanin, G., Synofzik, M., Timmerman, V., van de Warrenburg, B., van Os, N., Vandrovcova, J., Wilke, C., Bevot, A., Zuchner, S., Beltran, S., Laurie, S., Matalonga, L., Graessner, H., Zurek, B., Ellwanger, K., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., Hoischen, A., 't Hoen, P. A. C., Vissers, L. E. L. M., Gilissen, C., Steyaert, W., Sablauskas, K., de Voer, R. M., Janssen, E., de Boer, E., Steehouwer, M., Yaldiz, B., Kleefstra, T., Brookes, A. J., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Topf, A., Straub, V., Bettolo, C. M., Specht, S., Clayton-Smith, J., Banka, S., Alexander, E., Jackson, A., Faivre, L., Thauvin, C., Vitobello, A., Denomme-Pichon, A. -S., Duffourd, Y., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Gut, I. G., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Garcia, C., Fernandez-Callejo, M., Hernandez, C., Pico, D., Paramonov, I., Lochmuller, H., 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., Bonne, G., Evangelista, T., Allamand, V., Nelson, I., Yaou, R. B., Metay, C., Eymard, B., Cohen, E., Atalaia, A., Stojkovic, T., Macek, M., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Havlovicova, M., Kremlik, V., Parkinson, H., Keane, T., Spalding, D., Senf, A., Robinson, P., Danis, D., Robert, G., Costa, A., Patch, C., Hanna, M., Reilly, M., Muntoni, F., Zaharieva, I., Sarkozy, A., de Jonghe, P., Nigro, V., Banfi, S., Torella, A., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., 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 Velde, J. K., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Verloes, A., Drunat, S., Rooryck, C., Trimouille, A., Castello, R., Morleo, M., Pinelli, M., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., de la Rosa, F. J. A. G., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Renieri, A., Benetti, E., Molnar, M. J., Herzog, R., Pauly, M., Osorio, A. N., de Benito, D. N., Thompson, R., Polavarapu, K., Beeson, D., Cossins, J., Cruz, P. M. R., Hackman, P., Johari, M., Savarese, M., Udd, B., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Schrock, E., and Rump, A.
Abstract: In the original publication of the article, consortium author lists were missing in the article. The details are given below
Published: 2021

6. Recent advances in the pathology of heritable gastric cancer syndromes

Author: Gullo, I., Post, R.S. van der, Carneiro, F., Gullo, I., Post, R.S. van der, and Carneiro, F.
Abstract: Item does not contain fulltext
Published: 2021

7. Quantifying inflammation and fibrosis through a surgical histopathological score can differentiate ileal Crohn's disease phenotypes and predict postoperative progressive disease

Author: Tavares de Sousa, H., Gullo, I., Castelli, C., Dias, C. C., and Magro, F.
Subjects: Gastroenterology & Hepatology
Abstract: The quantification of fibrosis in Crohn’s disease (CD) still relies on surgical specimens’ pathology. We aimed to correlate quantification of inflammation and fibrosis of CD ileal resection specimens with postoperative progressive disease. info:eu-repo/semantics/publishedVersion
Published: 2020

8. Sometimes it is not what it seems: Animal-type melanoma, an unusual pigmented lesion of the scalp

Author: Menes M, Álvaro Silva, O. Oliveira, Gullo I, Costa C, and D. Barreiro
Subjects: Pathology, medicine.medical_specialty, medicine.anatomical_structure, business.industry, Scalp, Medicine, Pigmented lesion, General Medicine, business, Animal type melanoma
Published: 2020

9. Hereditary diffuse gastric cancer: updated clinical practice guidelines

Author: Blair, V.R., McLeod, M., Carneiro, F., Coit, D.G., D'Addario, J.L., Dieren, J.M. van, Harris, K.L., Hoogerbrugge, N., Oliveira, C. de, Post, R.S. van der, Arnold, J., Benusiglio, P.R., Bisseling, T.M., Boussioutas, A., Cats, A., Charlton, A., Schreiber, K.E., Davis, J.L., Pietro, M.D., Fitzgerald, R.C., Ford, J.M., Gamet, K., Gullo, I., Hardwick, R.H., Huntsman, D.G., Kaurah, P., Kupfer, S.S., Latchford, A., Mansfield, P.F., Nakajima, T., Parry, S., Rossaak, J., Sugimura, H., Svrcek, M., Tischkowitz, M., Ushijima, T., Yamada, H., Yang, H.Keri, Claydon, A., Figueiredo, J., Paringatai, K., Seruca, R., Bougen-Zhukov, N., Brew, T., Busija, S., Carneiro, P., DeGregorio, L., Fisher, H., Gardner, E., Godwin, T.D., Holm, K.N., Humar, B., Lintott, C.J., Monroe, E.C., Muller, M.D., Norero, E., Nouri, Y., Paredes, J., Sanches, J.M., Schulpen, E., Ribeiro, A.S., Sporle, A., Whitworth, J., Zhang, L., Reeve, A.E., Guilford, P., Blair, V.R., McLeod, M., Carneiro, F., Coit, D.G., D'Addario, J.L., Dieren, J.M. van, Harris, K.L., Hoogerbrugge, N., Oliveira, C. de, Post, R.S. van der, Arnold, J., Benusiglio, P.R., Bisseling, T.M., Boussioutas, A., Cats, A., Charlton, A., Schreiber, K.E., Davis, J.L., Pietro, M.D., Fitzgerald, R.C., Ford, J.M., Gamet, K., Gullo, I., Hardwick, R.H., Huntsman, D.G., Kaurah, P., Kupfer, S.S., Latchford, A., Mansfield, P.F., Nakajima, T., Parry, S., Rossaak, J., Sugimura, H., Svrcek, M., Tischkowitz, M., Ushijima, T., Yamada, H., Yang, H.Keri, Claydon, A., Figueiredo, J., Paringatai, K., Seruca, R., Bougen-Zhukov, N., Brew, T., Busija, S., Carneiro, P., DeGregorio, L., Fisher, H., Gardner, E., Godwin, T.D., Holm, K.N., Humar, B., Lintott, C.J., Monroe, E.C., Muller, M.D., Norero, E., Nouri, Y., Paredes, J., Sanches, J.M., Schulpen, E., Ribeiro, A.S., Sporle, A., Whitworth, J., Zhang, L., Reeve, A.E., and Guilford, P.
Abstract: Contains fulltext : 225261.pdf (Publisher’s version ) (Closed access), Hereditary diffuse gastric cancer (HDGC) is an autosomal dominant cancer syndrome that is characterised by a high prevalence of diffuse gastric cancer and lobular breast cancer. It is largely caused by inactivating germline mutations in the tumour suppressor gene CDH1, although pathogenic variants in CTNNA1 occur in a minority of families with HDGC. In this Policy Review, we present updated clinical practice guidelines for HDGC from the International Gastric Cancer Linkage Consortium (IGCLC), which recognise the emerging evidence of variability in gastric cancer risk between families with HDGC, the growing capability of endoscopic and histological surveillance in HDGC, and increased experience of managing long-term sequelae of total gastrectomy in young patients. To redress the balance between the accessibility, cost, and acceptance of genetic testing and the increased identification of pathogenic variant carriers, the HDGC genetic testing criteria have been relaxed, mainly through less restrictive age limits. Prophylactic total gastrectomy remains the recommended option for gastric cancer risk management in pathogenic CDH1 variant carriers. However, there is increasing confidence from the IGCLC that endoscopic surveillance in expert centres can be safely offered to patients who wish to postpone surgery, or to those whose risk of developing gastric cancer is not well defined.
Published: 2020

10. Hereditary diffuse gastric cancer: updated clinical practice guidelines

Author: Blair, VR, McLeod, M, Carneiro, F, Coit, DG, D'Addario, JL, van Dieren, JM, Harris, KL, Hoogerbrugge, N, Oliveira, C, van der Post, RS, Arnold, J, Benusiglio, PR, Bisseling, TM, Boussioutas, A, Cats, A, Charlton, A, Schreiber, KEC, Davis, JL, di Pietro, M, Fitzgerald, RC, Ford, JM, Gamet, K, Gullo, I, Hardwick, RH, Huntsman, DG, Kaurah, P, Kupfer, SS, Latchford, A, Mansfield, PF, Nakajima, T, Parry, S, Rossaak, J, Sugimura, H, Svrcek, M, Tischkowitz, M, Ushijima, T, Yamada, H, Yang, H-K, Claydon, A, Figueiredo, J, Paringatai, K, Seruca, R, Bougen-Zhukov, N, Brew, T, Busija, S, Carneiro, P, DeGregorio, L, Fisher, H, Gardner, E, Godwin, TD, Holm, KN, Humar, B, Lintott, CJ, Monroe, EC, Muller, MD, Norero, E, Nouri, Y, Paredes, J, Sanches, JM, Schulpen, E, Ribeiro, AS, Sporle, A, Whitworth, J, Zhang, L, Reeve, AE, Guilford, P, Blair, VR, McLeod, M, Carneiro, F, Coit, DG, D'Addario, JL, van Dieren, JM, Harris, KL, Hoogerbrugge, N, Oliveira, C, van der Post, RS, Arnold, J, Benusiglio, PR, Bisseling, TM, Boussioutas, A, Cats, A, Charlton, A, Schreiber, KEC, Davis, JL, di Pietro, M, Fitzgerald, RC, Ford, JM, Gamet, K, Gullo, I, Hardwick, RH, Huntsman, DG, Kaurah, P, Kupfer, SS, Latchford, A, Mansfield, PF, Nakajima, T, Parry, S, Rossaak, J, Sugimura, H, Svrcek, M, Tischkowitz, M, Ushijima, T, Yamada, H, Yang, H-K, Claydon, A, Figueiredo, J, Paringatai, K, Seruca, R, Bougen-Zhukov, N, Brew, T, Busija, S, Carneiro, P, DeGregorio, L, Fisher, H, Gardner, E, Godwin, TD, Holm, KN, Humar, B, Lintott, CJ, Monroe, EC, Muller, MD, Norero, E, Nouri, Y, Paredes, J, Sanches, JM, Schulpen, E, Ribeiro, AS, Sporle, A, Whitworth, J, Zhang, L, Reeve, AE, and Guilford, P
Abstract: Hereditary diffuse gastric cancer (HDGC) is an autosomal dominant cancer syndrome that is characterised by a high prevalence of diffuse gastric cancer and lobular breast cancer. It is largely caused by inactivating germline mutations in the tumour suppressor gene CDH1, although pathogenic variants in CTNNA1 occur in a minority of families with HDGC. In this Policy Review, we present updated clinical practice guidelines for HDGC from the International Gastric Cancer Linkage Consortium (IGCLC), which recognise the emerging evidence of variability in gastric cancer risk between families with HDGC, the growing capability of endoscopic and histological surveillance in HDGC, and increased experience of managing long-term sequelae of total gastrectomy in young patients. To redress the balance between the accessibility, cost, and acceptance of genetic testing and the increased identification of pathogenic variant carriers, the HDGC genetic testing criteria have been relaxed, mainly through less restrictive age limits. Prophylactic total gastrectomy remains the recommended option for gastric cancer risk management in pathogenic CDH1 variant carriers. However, there is increasing confidence from the IGCLC that endoscopic surveillance in expert centres can be safely offered to patients who wish to postpone surgery, or to those whose risk of developing gastric cancer is not well defined.
Published: 2020

11. P051 Quantifying inflammation and fibrosis through a surgical histopathological score can differentiate ileal Crohn’s disease phenotypes and predict postoperative progressive disease

Author: Tavares de Sousa, H, primary, Gullo, I, additional, Castelli, C, additional, Dias, C C, additional, and Magro, F, additional
Published: 2020
Full Text: View/download PDF

12. Spectral Approximation for Wind Induced Structural Vibration Studies

Author: Gullo, I., Paola, M. Di, and Spanos, Pol D.
Published: 1998
Full Text: View/download PDF

13. Molecular subtypes of metastatic (met) gastric cancer (GC) (MoTriGastric): New biomarkers closer to the clinics

Author: Alsina Maqueda, M., primary, Ruiz, F., additional, Landolfi, S., additional, Viaplana, C., additional, Miquel, J.M., additional, Jimenez, J., additional, Diez, M., additional, Gullo, I., additional, Mirallas, O., additional, Tabernero, J., additional, Carneiro, F., additional, Nuciforo, P.G., additional, Vivancos, A., additional, and Dienstmann, R., additional
Published: 2019
Full Text: View/download PDF

14. Digital generation of multivariate wind field processes

Author: Di Paola, M. and Gullo, I.
Published: 2001
Full Text: View/download PDF

15. Gastric carcinoma with lymphoid stroma in the era of the immune context and immunotherapies

Author: Gullo, I, Gonçalves, G, Athelogou, M, Pinto, ML, Almeida, GM, Oliveira, C, and Carneiro, F
Abstract: Poster presented at the 5th Annual Meeting (3-4 of Novembre, 2016; placed in Axis Vermar Conference & Beach Hotal, Póvoa de Varzim, Portugal)
Published: 2016
Full Text: View/download PDF

16. Histopathological, Molecular, and Genetic Profile of Hereditary Diffuse Gastric Cancer: Current Knowledge and Challenges for the Future

Author: Post, R.S. van der, Gullo, I., Oliveira, C. de, Tang, L.H., Grabsch, H.I., O'Donovan, M., Fitzgerald, R.C., Krieken, H. van, and Carneiro, F.
Subjects: Cancer development and immune defence Radboud Institute for Molecular Life Sciences [Radboudumc 2], digestive system diseases
Abstract: Contains fulltext : 172687.pdf (Publisher’s version ) (Closed access) Familial clustering is seen in 10 % of gastric cancer cases and approximately 1-3 % of gastric cancer arises in the setting of hereditary diffuse gastric cancer (HDGC). In families with HDGC, gastric cancer presents at young age. HDGC is predominantly caused by germline mutations in CDH1 and in a minority by mutations in other genes, including CTNNA1. Early stage HDGC is characterized by a few, up to dozens of intramucosal foci of signet ring cell carcinoma and its precursor lesions. These include in situ signet ring cell carcinoma and pagetoid spread of signet ring cells. Advanced HDGC presents as poorly cohesive/diffuse type carcinoma, normally with very few typical signet ring cells, and has a poor prognosis. Currently, it is unknown which factors drive the progression towards aggressive disease, but it is clear that most intramucosal lesions will not have such progression.Immunohistochemical profile of early and advanced HDGC is often characterized by abnormal E-cadherin immunoexpression, including absent or reduced membranous expression, as well as "dotted" or cytoplasmic expression. However, membranous expression of E-cadherin does not exclude HDGC. Intramucosal HDGC (pT1a) presents with an "indolent" phenotype, characterized by typical signet ring cells without immunoexpression of Ki-67 and p53, while advanced carcinomas (pT > 1) display an "aggressive" phenotype with pleomorphic cells, that are immunoreactive for Ki-67 and p53. These features show that the IHC profile is different between intramucosal and more advanced HDGC, providing evidence of phenotypic heterogeneity, and may help to define predictive biomarkers of progression from indolent to aggressive, widely invasive carcinomas.
Published: 2016

17. Angiogenesis and inflammation at the crossroads between diabetes and cancer

Author: Rocha, R., primary, Rodrigues, I., additional, Gullo, I., additional, Gonçalves, G., additional, Pedro, J., additional, Carvalho, D., additional, Carneiro, F., additional, Soares, R., additional, and Andrade, S., additional
Published: 2017
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18. Intratumoral heterogeneity in gastric cancer: a new challenge to face

Author: Alsina, M., primary, Gullo, I., additional, and Carneiro, F., additional
Published: 2017
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19. Abstracts from the 4th ImmunoTherapy of Cancer Conference

Author: Ženka, J., primary, Caisová, V., additional, Uher, O., additional, Nedbalová, P., additional, Kvardová, K., additional, Masáková, K., additional, Krejčová, G., additional, Paďouková, L., additional, Jochmanová, I., additional, Wolf, K. I., additional, Chmelař, J., additional, Kopecký, J., additional, Loumagne, L., additional, Mestadier, J., additional, D’agostino, S., additional, Rohaut, A., additional, Ruffin, Y., additional, Croize, V., additional, Lemaître, O., additional, Sidhu, S. S., additional, Althammer, S., additional, Steele, K., additional, Rebelatto, M., additional, Tan, T., additional, Wiestler, T., additional, Spitzmueller, A., additional, Korn, R., additional, Schmidt, G., additional, Higgs, B., additional, Li, X., additional, Shi, L., additional, Jin, X., additional, Ranade, K., additional, Koeck, S., additional, Amann, A., additional, Gamerith, G., additional, Zwierzina, M., additional, Lorenz, E., additional, Zwierzina, H., additional, Kern, J., additional, Riva, M., additional, Baert, T., additional, Coosemans, A., additional, Giovannoni, R., additional, Radaelli, E., additional, Gsell, W., additional, Himmelreich, U., additional, Van Ranst, M., additional, Xing, F., additional, Qian, W., additional, Dong, C., additional, Xu, X., additional, Guo, S., additional, Shi, Q., additional, Quandt, D., additional, Seliger, B., additional, Plett, C., additional, Amberger, D. C., additional, Rabe, A., additional, Deen, D., additional, Stankova, Z., additional, Hirn, A., additional, Vokac, Y., additional, Werner, J., additional, Krämer, D., additional, Rank, A., additional, Schmid, C., additional, Schmetzer, H., additional, Guerin, M., additional, Weiss, J. M., additional, Regnier, F., additional, Renault, G., additional, Vimeux, L., additional, Peranzoni, E., additional, Feuillet, V., additional, Thoreau, M., additional, Guilbert, T., additional, Trautmann, A., additional, Bercovici, N., additional, Doraneh-Gard, F., additional, Boeck, C. L., additional, Gunsilius, C., additional, Kugler, C., additional, Schmohl, J., additional, Kraemer, D., additional, Ismann, B., additional, Schmetzer, H. M., additional, Markota, A., additional, Ochs, C., additional, May, P., additional, Gottschlich, A., additional, Gosálvez, J. Suárez, additional, Karches, C., additional, Wenk, D., additional, Endres, S., additional, Kobold, S., additional, Hilmenyuk, T., additional, Klar, R., additional, Jaschinski, F., additional, Augustin, F., additional, Manzl, C., additional, Hoflehner, E., additional, Moser, P., additional, Zelger, B., additional, Köck, S., additional, Schäfer, G., additional, Öfner, D., additional, Maier, H., additional, Sopper, S., additional, Prado-Garcia, H., additional, Romero-Garcia, S., additional, Sandoval-Martínez, R., additional, Puerto-Aquino, A., additional, Lopez-Gonzalez, J., additional, Rumbo-Nava, U., additional, Van Hoylandt, A., additional, Busschaert, P., additional, Vergote, I., additional, Laengle, J., additional, Pilatova, K., additional, Budinska, E., additional, Bencsikova, B., additional, Sefr, R., additional, Nenutil, R., additional, Brychtova, V., additional, Fedorova, L., additional, Hanakova, B., additional, Zdrazilova-Dubska, L., additional, Allen, Chris, additional, Ku, Yuan-Chieh, additional, Tom, Warren, additional, Sun, Yongming, additional, Pankov, Alex, additional, Looney, Tim, additional, Hyland, Fiona, additional, Au-Young, Janice, additional, Mongan, Ann, additional, Becker, A., additional, Tan, J. B. L., additional, Chen, A., additional, Lawson, K., additional, Lindsey, E., additional, Powers, J. P., additional, Walters, M., additional, Schindler, U., additional, Young, S., additional, Jaen, J. C., additional, Yin, S., additional, Chen, Y., additional, Gullo, I., additional, Gonçalves, G., additional, Pinto, M. L., additional, Athelogou, M., additional, Almeida, G., additional, Huss, R., additional, Oliveira, C., additional, Carneiro, F., additional, Merz, C., additional, Sykora, J., additional, Hermann, K., additional, Hussong, R., additional, Richards, D. M., additional, Fricke, H., additional, Hill, O., additional, Gieffers, C., additional, Pinho, M. P., additional, Barbuto, J. A. M., additional, McArdle, S. E., additional, Foulds, G., additional, Vadakekolathu, J. N., additional, Abdel-Fatah, T. M. A., additional, Johnson, C., additional, Hood, S., additional, Moseley, P., additional, Rees, R. C., additional, Chan, S. Y. T., additional, Pockley, A. G., additional, Rutella, S., additional, Geppert, C., additional, Hartmann, A., additional, Kumar, K. Senthil, additional, Gokilavani, M., additional, Wang, S., additional, Redondo-Müller, M., additional, Heinonen, K., additional, Marschall, V., additional, Thiemann, M., additional, Zhang, L., additional, Mao, B., additional, Jin, Y., additional, Zhai, G., additional, Li, Z., additional, Wang, Z., additional, An, X., additional, Qiao, M., additional, Zhang, J., additional, Weber, J., additional, Kluger, H., additional, Halaban, R., additional, Sznol, M., additional, Roder, H., additional, Roder, J., additional, Grigorieva, J., additional, Asmellash, S., additional, Meyer, K., additional, Steingrimsson, A., additional, Blackmon, S., additional, Sullivan, R., additional, Sutanto, W., additional, Guenther, T., additional, Schuster, F., additional, Salih, H., additional, Babor, F., additional, Borkhardt, A., additional, Kim, Y., additional, Oh, I., additional, Park, C., additional, Ahn, S., additional, Na, K., additional, Song, S., additional, Choi, Y., additional, Poprach, A., additional, Lakomy, R., additional, Selingerova, I., additional, Demlova, R., additional, Kozakova, S., additional, Valik, D., additional, Petrakova, K., additional, Vyzula, R., additional, Aguilar-Cazares, D., additional, Galicia-Velasco, M., additional, Camacho-Mendoza, C., additional, Islas-Vazquez, L., additional, Chavez-Dominguez, R., additional, Gonzalez-Gonzalez, C., additional, Lopez-Gonzalez, J. S., additional, Yang, S., additional, Moynihan, K. D., additional, Noh, M., additional, Bekdemir, A., additional, Stellacci, F., additional, Irvine, D. J., additional, Volz, B., additional, Kapp, K., additional, Oswald, D., additional, Wittig, B., additional, Schmidt, M., additional, Kleef, R., additional, Bohdjalian, A., additional, McKee, D., additional, Moss, R. W., additional, Saeed, Mesha, additional, Zalba, Sara, additional, Debets, Reno, additional, ten Hagen, Timo L. M., additional, Javed, S., additional, Becher, J., additional, Koch-Nolte, F., additional, Haag, F., additional, Gordon, E. M., additional, Sankhala, K. K., additional, Stumpf, N., additional, Tseng, W., additional, Chawla, S. P., additional, Suárez, N. González, additional, Báez, G. Bergado, additional, Rodríguez, M. Cruz, additional, Pérez, A. Gutierrez, additional, García, L. Chao, additional, Fernández, D. Hernández, additional, Pous, J. Raymond, additional, Ramírez, B. Sánchez, additional, Jacoberger-Foissac, C., additional, Saliba, H., additional, Seguin, C., additional, Brion, A., additional, Frisch, B., additional, Fournel, S., additional, Heurtault, B., additional, Otterhaug, T., additional, Håkerud, M., additional, Nedberg, A., additional, Edwards, V., additional, Selbo, P., additional, Høgset, A., additional, Jaitly, T., additional, Dörrie, J., additional, Schaft, N., additional, Gross, S., additional, Schuler-Thurner, B., additional, Gupta, S., additional, Taher, L., additional, Schuler, G., additional, Vera, J., additional, Rataj, F., additional, Kraus, F., additional, Grassmann, S., additional, Chaloupka, M., additional, Lesch, S., additional, Heise, C., additional, Cadilha, B. M. Loureiro, additional, and Dorman, K., additional
Published: 2017
Full Text: View/download PDF

20. 823P - Molecular subtypes of metastatic (met) gastric cancer (GC) (MoTriGastric): New biomarkers closer to the clinics

Author: Alsina Maqueda, M., Ruiz, F., Landolfi, S., Viaplana, C., Miquel, J.M., Jimenez, J., Diez, M., Gullo, I., Mirallas, O., Tabernero, J., Carneiro, F., Nuciforo, P.G., Vivancos, A., and Dienstmann, R.
Published: 2019
Full Text: View/download PDF

21. Minimum biopsy set for HER-2 evaluation in gastro-esophageal adenocarcinoma

Author: Grillo, Federica, Mastracci, Luca, Gullo, I, Piol, N, Molinaro, L, Fassan, M, Rugge, M, and Fiocca, Roberto
Published: 2013

22. Probability density function of the non-gaussian alongwind response of SDOF linear structures

Author: Gullo, I., Muscolino, Giuseppe Alfredo, and Vasta, M.
Published: 1997

23. Non-Gaussian probability density function of SDOF linear structures under wind actions

Author: Gullo, I., primary, Muscolino, G., additional, and Vasta, M., additional
Published: 1998
Full Text: View/download PDF

24. Digital generation of multivariate wind field processes

Author: Paola, M. Di and Gullo, I.
Published: 2001
Full Text: View/download PDF

25. Endoscopic submucosal dissection of a schwann cell hamartoma mimicking a lateral spreading tumor of the rectum

Author: Gaspar, R., João Santos-Antunes, Marques, M., Gullo, I., Silva, R., Lopes, J., and Macedo, G.

26. Morphological and immunohistochemical profile of hereditary diffuse gastric cancer

Author: Gullo, I., Post, R. S., Oliveira, C., Tang, L. H., Grabsch, H., O Donovan, M., Fitzgerald, R., Krieken, H., and Fatima Carneiro

27. Gastric carcinoma with lymphoid stroma: A study of Epstein-Barr virus, microsatellite instability, tumour immune microenvironment and PD-L1 expression

Author: Gullo, I., Goncalves, G., Pinto, M., Machado, F., Almeida, G. M., Oliveira, C., and Fatima Carneiro

28. Abstracts from the 4th ImmunoTherapy of Cancer Conference

Author: Ženka, J., Caisová, V., Uher, O., Nedbalová, P., Kvardová, K., Masáková, K., Krejčová, G., Paďouková, L., Jochmanová, I., Wolf, K. I., Chmelař, J., Kopecký, J., Loumagne, L., Mestadier, J., D’agostino, S., Rohaut, A., Ruffin, Y., Croize, V., Lemaître, O., Sidhu, S. S., Althammer, S., Steele, K., Rebelatto, M., Tan, T., Wiestler, T., Spitzmueller, A., Korn, R., Schmidt, G., Higgs, B., Li, X., Shi, L., Jin, X., Ranade, K., Koeck, S., Amann, A., Gamerith, G., Zwierzina, M., Lorenz, E., Zwierzina, H., Kern, J., Riva, M., Baert, T., Coosemans, A., Giovannoni, R., Radaelli, E., Gsell, W., Himmelreich, U., Van Ranst, M., Xing, F., Qian, W., Dong, C., Xu, X., Guo, S., Shi, Q., Quandt, D., Seliger, B., Plett, C., Amberger, D. C., Rabe, A., Deen, D., Stankova, Z., Hirn, A., Vokac, Y., Werner, J., Krämer, D., Rank, A., Schmid, C., Schmetzer, H., Guerin, M., Weiss, J. M., Regnier, F., Renault, G., Vimeux, L., Peranzoni, E., Feuillet, V., Thoreau, M., Guilbert, T., Trautmann, A., Bercovici, N., Doraneh-Gard, F., Boeck, C. L., Gunsilius, C., Kugler, C., Schmohl, J., Kraemer, D., Ismann, B., Schmetzer, H. M., Markota, A., Ochs, C., May, P., Gottschlich, A., Gosálvez, J. Suárez, Karches, C., Wenk, D., Endres, S., Kobold, S., Hilmenyuk, T., Klar, R., Jaschinski, F., Augustin, F., Manzl, C., Hoflehner, E., Moser, P., Zelger, B., Köck, S., Schäfer, G., Öfner, D., Maier, H., Sopper, S., Prado-Garcia, H., Romero-Garcia, S., Sandoval-Martínez, R., Puerto-Aquino, A., Lopez-Gonzalez, J., Rumbo-Nava, U., Van Hoylandt, A., Busschaert, P., Vergote, I., Laengle, J., Pilatova, K., Budinska, E., Bencsikova, B., Sefr, R., Nenutil, R., Brychtova, V., Fedorova, L., Hanakova, B., Zdrazilova-Dubska, L., Allen, Chris, Ku, Yuan-Chieh, Tom, Warren, Sun, Yongming, Pankov, Alex, Looney, Tim, Hyland, Fiona, Au-Young, Janice, Mongan, Ann, Becker, A., Tan, J. B. L., Chen, A., Lawson, K., Lindsey, E., Powers, J. P., Walters, M., Schindler, U., Young, S., Jaen, J. C., Yin, S., Chen, Y., Gullo, I., Gonçalves, G., Pinto, M. L., Athelogou, M., Almeida, G., Huss, R., Oliveira, C., Carneiro, F., Merz, C., Sykora, J., Hermann, K., Hussong, R., Richards, D. M., Fricke, H., Hill, O., Gieffers, C., Pinho, M. P., Barbuto, J. A. M., McArdle, S. E., Foulds, G., Vadakekolathu, J. N., Abdel-Fatah, T. M. A., Johnson, C., Hood, S., Moseley, P., Rees, R. C., Chan, S. Y. T., Pockley, A. G., Rutella, S., Geppert, C., Hartmann, A., Kumar, K. Senthil, Gokilavani, M., Wang, S., Redondo-Müller, M., Heinonen, K., Marschall, V., Thiemann, M., Zhang, L., Mao, B., Jin, Y., Zhai, G., Li, Z., Wang, Z., An, X., Qiao, M., Zhang, J., Weber, J., Kluger, H., Halaban, R., Sznol, M., Roder, H., Roder, J., Grigorieva, J., Asmellash, S., Meyer, K., Steingrimsson, A., Blackmon, S., Sullivan, R., Sutanto, W., Guenther, T., Schuster, F., Salih, H., Babor, F., Borkhardt, A., Kim, Y., Oh, I., Park, C., Ahn, S., Na, K., Song, S., Choi, Y., Poprach, A., Lakomy, R., Selingerova, I., Demlova, R., Kozakova, S., Valik, D., Petrakova, K., Vyzula, R., Aguilar-Cazares, D., Galicia-Velasco, M., Camacho-Mendoza, C., Islas-Vazquez, L., Chavez-Dominguez, R., Gonzalez-Gonzalez, C., Lopez-Gonzalez, J. S., Yang, S., Moynihan, K. D., Noh, M., Bekdemir, A., Stellacci, F., Irvine, D. J., Volz, B., Kapp, K., Oswald, D., Wittig, B., Schmidt, M., Kleef, R., Bohdjalian, A., McKee, D., Moss, R. W., Saeed, Mesha, Zalba, Sara, Debets, Reno, ten Hagen, Timo L. M., Javed, S., Becher, J., Koch-Nolte, F., Haag, F., Gordon, E. M., Sankhala, K. K., Stumpf, N., Tseng, W., Chawla, S. P., Suárez, N. González, Báez, G. Bergado, Rodríguez, M. Cruz, Pérez, A. Gutierrez, García, L. Chao, Fernández, D. Hernández, Pous, J. Raymond, Ramírez, B. Sánchez, Jacoberger-Foissac, C., Saliba, H., Seguin, C., Brion, A., Frisch, B., Fournel, S., Heurtault, B., Otterhaug, T., Håkerud, M., Nedberg, A., Edwards, V., Selbo, P., Høgset, A., Jaitly, T., Dörrie, J., Schaft, N., Gross, S., Schuler-Thurner, B., Gupta, S., Taher, L., Schuler, G., Vera, J., Rataj, F., Kraus, F., Grassmann, S., Chaloupka, M., Lesch, S., Heise, C., Cadilha, B. M. Loureiro, and Dorman, K.
Subjects: Meeting Abstracts
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29. Precursor lesions of hereditary diffuse gastric cancer (HDGC) in prophylactic gastrectomies performed in carriers of CDH1 germline mutations. The experience of a reference center

Author: Wen, X., Gullo, I., and Fatima Carneiro

30. KRAS mutations in microsatellite instable gastric tumours: impact of targeted treatment and intratumoural heterogeneity

Author: Queirós P, Hugo Pinheiro, Carvalho J, Oliveira P, Gullo I, Carneiro F, Gm, Almeida, and Oliveira C

31. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related Autosomal Recessive Ectodermal Dysplasia 14

Author: Adam Jackson, Sheng-Jia Lin, Elizabeth A. Jones, Kate E. Chandler, David Orr, Celia Moss, Zahra Haider, Gavin Ryan, Simon Holden, Mike Harrison, Nigel Burrows, Wendy D. Jones, Mary Loveless, Cassidy Petree, Helen Stewart, Karen Low, Deirdre Donnelly, Simon Lovell, Konstantina Drosou, Gaurav K. Varshney, Siddharth Banka, J.C. Ambrose, P. Arumugam, R. Bevers, M. Bleda, F. Boardman-Pretty, C.R. Boustred, H. Brittain, M.A. Brown, M.J. Caulfield, G.C. Chan, A. Giess, J.N. Griffin, A. Hamblin, S. Henderson, T.J.P. Hubbard, R. Jackson, L.J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, A. Lakey, S.E.A. Leigh, I.U.S. Leong, F.J. Lopez, F. Maleady-Crowe, M. McEntagart, F. Minneci, J. Mitchell, L. Moutsianas, M. Mueller, N. Murugaesu, A.C. Need, P. O‘Donovan, C.A. Odhams, C. Patch, D. Perez-Gil, M.B. Pereira, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R.H. Scott, A. Siddiq, A. Sieghart, S.C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, A.L. Taylor Tavares, E.R.A. Thomas, S.R. Thompson, A. Tucci, M.J. Welland, E. Williams, K. Witkowska, S.M. Wood, M. Zarowiecki, Olaf Riess, Tobias B. Haack, Holm Graessner, Birte Zurek, Kornelia Ellwanger, Stephan Ossowski, German Demidov, Marc Sturm, Julia M. Schulze-Hentrich, Rebecca Schüle, Christoph Kessler, Melanie Wayand, Matthis Synofzik, Carlo Wilke, Andreas Traschütz, Ludger Schöls, Holger Hengel, Peter Heutink, Han Brunner, Hans Scheffer, Nicoline Hoogerbrugge, Alexander Hoischen, Peter A.C. ’t Hoen, Lisenka E.L.M. Vissers, Christian Gilissen, Wouter Steyaert, Karolis Sablauskas, Richarda M. de Voer, Erik-Jan Kamsteeg, Bart van de Warrenburg, Nienke van Os, Iris te Paske, Erik Janssen, Elke de Boer, Marloes Steehouwer, Burcu Yaldiz, Tjitske Kleefstra, Anthony J. Brookes, Colin Veal, Spencer Gibson, Marc Wadsley, Mehdi Mehtarizadeh, Umar Riaz, Greg Warren, Farid Yavari Dizjikan, Thomas Shorter, Ana Töpf, Volker Straub, Chiara Marini Bettolo, Sabine Specht, Jill Clayton-Smith, Elizabeth Alexander, Laurence Faivre, Christel Thauvin, Antonio Vitobello, Anne-Sophie Denommé-Pichon, Yannis Duffourd, Emilie Tisserant, Ange-Line Bruel, Christine Peyron, Aurore Pélissier, Sergi Beltran, Ivo Glynne Gut, Steven Laurie, Davide Piscia, Leslie Matalonga, Anastasios Papakonstantinou, Gemma Bullich, Alberto Corvo, Carles Garcia, Marcos Fernandez-Callejo, Carles Hernández, Daniel Picó, Ida Paramonov, Hanns Lochmüller, Gulcin Gumus, Virginie Bros-Facer, Ana Rath, Marc Hanauer, Annie Olry, David Lagorce, Svitlana Havrylenko, Katia Izem, Fanny Rigour, Giovanni Stevanin, Alexandra Durr, Claire-Sophie Davoine, Léna Guillot-Noel, Anna Heinzmann, Giulia Coarelli, Gisèle Bonne, Teresinha Evangelista, Valérie Allamand, Isabelle Nelson, Rabah Ben Yaou, Corinne Metay, Bruno Eymard, Enzo Cohen, Antonio Atalaia, Tanya Stojkovic, Milan Macek, Marek Turnovec, Dana Thomasová, Radka Pourová Kremliková, Vera Franková, Markéta Havlovicová, Vlastimil Kremlik, Helen Parkinson, Thomas Keane, Dylan Spalding, Alexander Senf, Peter Robinson, Daniel Danis, Glenn Robert, Alessia Costa, Christine Patch, Mike Hanna, Henry Houlden, Mary Reilly, Jana Vandrovcova, Francesco Muntoni, Irina Zaharieva, Anna Sarkozy, Vincent Timmerman, Jonathan Baets, Liedewei Van de Vondel, Danique Beijer, Peter de Jonghe, Vincenzo Nigro, Sandro Banfi, Annalaura Torella, Francesco Musacchia, Giulio Piluso, Alessandra Ferlini, Rita Selvatici, Rachele Rossi, Marcella Neri, Stefan Aretz, Isabel Spier, Anna Katharina Sommer, Sophia Peters, Carla Oliveira, Jose Garcia Pelaez, Ana Rita Matos, Celina São José, Marta Ferreira, Irene Gullo, Susana Fernandes, Luzia Garrido, Pedro Ferreira, Fátima Carneiro, Morris A. Swertz, Lennart Johansson, Joeri K. van der Velde, Gerben van der Vries, Pieter B. Neerincx, Dieuwke Roelofs-Prins, Sebastian Köhler, Alison Metcalfe, Alain Verloes, Séverine Drunat, Caroline Rooryck, Aurelien Trimouille, Raffaele Castello, Manuela Morleo, Michele Pinelli, Alessandra Varavallo, Manuel Posada De la Paz, Eva Bermejo Sánchez, Estrella López Martín, Beatriz Martínez Delgado, F. Javier Alonso García de la Rosa, Andrea Ciolfi, Bruno Dallapiccola, Simone Pizzi, Francesca Clementina Radio, Marco Tartaglia, Alessandra Renieri, Elisa Benetti, Peter Balicza, Maria Judit Molnar, Ales Maver, Borut Peterlin, Alexander Münchau, Katja Lohmann, Rebecca Herzog, Martje Pauly, Alfons Macaya, Anna Marcé-Grau, Andres Nascimiento Osorio, Daniel Natera de Benito, Rachel Thompson, Kiran Polavarapu, David Beeson, Judith Cossins, Pedro M. Rodriguez Cruz, Peter Hackman, Mridul Johari, Marco Savarese, Bjarne Udd, Rita Horvath, Gabriel Capella, Laura Valle, Elke Holinski-Feder, Andreas Laner, Verena Steinke-Lange, Evelin Schröck, Andreas Rump, Jackson, A., Lin, S. -J., Jones, E. A., Chandler, K. E., Orr, D., Moss, C., Haider, Z., Ryan, G., Holden, S., Harrison, M., Burrows, N., Jones, W. D., Loveless, M., Petree, C., Stewart, H., Low, K., Donnelly, D., Lovell, S., Drosou, K., Ambrose, J. C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C. R., Brittain, H., Brown, M. A., Caulfield, M. J., Chan, G. C., Giess, A., Griffin, J. N., Hamblin, A., Henderson, S., Hubbard, T. J. P., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Lakey, A., Leigh, S. E. A., Leong, I. U. S., Lopez, F. J., Maleady-Crowe, F., Mcentagart, M., Minneci, F., Mitchell, J., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., O'Donovan, P., Odhams, C. A., Patch, C., Perez-Gil, D., Pereira, M. B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R. H., Siddiq, A., Sieghart, A., Smith, S. C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A. L., Thomas, E. R. A., Thompson, S. R., Tucci, A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Zarowiecki, M., Riess, O., Haack, T. B., Graessner, H., Zurek, B., Ellwanger, K., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Schule, R., Kessler, C., Wayand, M., Synofzik, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., Hoischen, A., 't Hoen, P. A. C., Vissers, L. E. L. M., Gilissen, C., Steyaert, W., Sablauskas, K., de Voer, R. M., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., Paske, I. T., Janssen, E., de Boer, E., Steehouwer, M., Yaldiz, B., Kleefstra, T., Brookes, A. J., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Topf, A., Straub, V., Bettolo, C. M., Specht, S., Clayton-Smith, J., Banka, S., Alexander, E., Faivre, L., Thauvin, C., Vitobello, A., Denomme-Pichon, A. -S., Duffourd, Y., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Beltran, S., Gut, I. G., Laurie, S., Piscia, D., Matalonga, L., Papakonstantinou, A., Bullich, G., Corvo, A., Garcia, C., Fernandez-Callejo, M., Hernandez, C., Pico, D., Paramonov, I., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Olry, A., Lagorce, D., Havrylenko, S., Izem, K., Rigour, F., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Nelson, I., Ben Yaou, R., Metay, C., Eymard, B., Cohen, E., Atalaia, A., Stojkovic, T., Macek, M., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Havlovicova, M., Kremlik, V., Parkinson, H., Keane, T., Spalding, D., Senf, A., Robinson, P., Danis, D., Robert, G., Costa, A., Hanna, M., Houlden, H., Reilly, M., Vandrovcova, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., Van de Vondel, L., Beijer, D., de Jonghe, P., Nigro, V., Banfi, S., Torella, A., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., 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 Velde, J. K., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Verloes, A., Drunat, S., Rooryck, C., Trimouille, A., Castello, R., Morleo, M., Pinelli, M., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., Alonso Garcia de la Rosa, F. J., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Renieri, A., Benetti, E., Balicza, P., Molnar, M. J., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., Macaya, A., Marce-Grau, A., Osorio, A. N., Natera de Benito, D., Thompson, R., Polavarapu, K., Beeson, D., Cossins, J., Rodriguez Cruz, P. M., Hackman, P., Johari, M., Savarese, M., Udd, B., Horvath, R., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Schrock, E., Rump, A., and Varshney, G. K.
Subjects: Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Hypodontia, Closca, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Ectodermal dysplasia, TSPEAR, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], Conical teeth, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Article, Enamel knot, Autosomal recessive ectodermal dysplasia type 14, WNT10A, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Extracellular matrix dependant signalling, Molecular Medicine, zebrafish fin regeneration, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Genetics (clinical)
Abstract: Item does not contain fulltext TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara (-/-);tspearb (-/-) double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.
Published: 2023

32. 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

33. Solve-RD: systematic pan-European data sharing and collaborative analysis to solve rare diseases

Author: Zurek, Birte, Ellwanger, Kornelia, Vissers, Lisenka E. L. M., Schüle, Rebecca, Synofzik, Matthis, Töpf, Ana, de Voer, Richarda M., Laurie, Steven, Matalonga, Leslie, Gilissen, Christian, Ossowski, Stephan, ’t Hoen, Peter A. C., Vitobello, Antonio, Schulze-Hentrich, Julia M., Riess, Olaf, Brunner, Han G., Brookes, Anthony J., Rath, Ana, Bonne, Gisèle, Gumus, Gulcin, Verloes, Alain, Hoogerbrugge, Nicoline, Evangelista, Teresinha, Harmuth, Tina, Swertz, Morris, Spalding, Dylan, Hoischen, Alexander, Beltran, Sergi, Graessner, Holm, Haack, Tobias B., Demidov, German, Sturm, Marc, Kessler, Christoph, Wayand, Melanie, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Heutink, Peter, Brunner, Han, Scheffer, Hans, Steyaert, Wouter, Sablauskas, Karolis, Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, te Paske, Iris, Janssen, Erik, de Boer, Elke, Steehouwer, Marloes, Yaldiz, Burcu, Kleefstra, Tjitske, Veal, Colin, Gibson, Spencer, Wadsley, Marc, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Specht, Sabine, Clayton-Smith, Jill, Banka, Siddharth, Alexander, Elizabeth, Jackson, Adam, Faivre, Laurence, Thauvin, Christel, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Tisserant, Emilie, Bruel, Ange-Line, Peyron, Christine, Pélissier, Aurore, Gut, Ivo Glynne, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Garcia, Carles, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Paramonov, Ida, Lochmüller, Hanns, Bros-Facer, Virginie, Hanauer, Marc, Olry, Annie, Lagorce, David, Havrylenko, Svitlana, Izem, Katia, Rigour, Fanny, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Allamand, Valérie, Nelson, Isabelle, Yaou, Rabah Ben, Metay, Corinne, Eymard, Bruno, Cohen, Enzo, Atalaia, Antonio, Stojkovic, Tanya, Macek, Milan, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Kremlik, Vlastimil, Parkinson, Helen, Keane, Thomas, Senf, Alexander, Robinson, Peter, Danis, Daniel, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Vandrovcova, Jana, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, Van de Vondel, Liedewei, Beijer, Danique, de Jonghe, Peter, Nigro, Vincenzo, Banfi, Sandro, Torella, Annalaura, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Rossi, Rachele, Neri, Marcella, Aretz, Stefan, Spier, Isabel, Sommer, Anna Katharina, 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 Velde, Joeri K., van der Vries, Gerben, Neerincx, Pieter B., Roelofs-Prins, Dieuwke, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Rooryck, Caroline, Trimouille, Aurelien, Castello, Raffaele, Morleo, Manuela, Pinelli, Michele, Varavallo, Alessandra, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Martín, Estrella López, Delgado, Beatriz Martínez, de la Rosa, F. Javier Alonso García, Ciolfi, Andrea, Dallapiccola, Bruno, Pizzi, Simone, Radio, Francesca Clementina, Tartaglia, Marco, Renieri, Alessandra, Benetti, Elisa, Balicza, Peter, Molnar, Maria Judit, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, Macaya, Alfons, Marcé-Grau, Anna, Osorio, Andres Nascimiento, de Benito, Daniel Natera, Thompson, Rachel, Polavarapu, Kiran, Beeson, David, Cossins, Judith, Cruz, Pedro M. Rodriguez, Hackman, Peter, Johari, Mridul, Savarese, Marco, Udd, Bjarne, Horvath, Rita, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Schröck, Evelin, Rump, Andreas, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), RS: GROW - R4 - Reproductive and Perinatal Medicine, Klinische Genetica, MUMC+: DA Klinische Genetica (5), Zurek, Birte [0000-0002-8200-7542], Ellwanger, Kornelia [0000-0003-4845-5795], Vissers, Lisenka ELM [0000-0001-6470-5497], Synofzik, Matthis [0000-0002-2280-7273], de Voer, Richarda M [0000-0002-8222-0343], Laurie, Steven [0000-0003-3913-5829], Gilissen, Christian [0000-0003-1693-9699], 't Hoen, Peter AC [0000-0003-4450-3112], Vitobello, Antonio [0000-0003-3717-8374], Brookes, Anthony J [0000-0001-8686-0017], Rath, Ana [0000-0003-4308-6337], Bonne, Gisèle [0000-0002-2516-3258], Verloes, Alain [0000-0003-4819-0264], Hoogerbrugge, Nicoline [0000-0003-2393-8141], Harmuth, Tina [0000-0002-4833-8057], Spalding, Dylan [0000-0002-4285-2493], Beltran, Sergi [0000-0002-2810-3445], Graessner, Holm [0000-0001-9803-7183], Apollo - University of Cambridge Repository, Zurek, B., Ellwanger, K., Vissers, L. E. L. M., Schule, R., Synofzik, M., Topf, A., de Voer, R. M., Laurie, S., Matalonga, L., Gilissen, C., Ossowski, S., 't Hoen, P. A. C., Vitobello, A., Schulze-Hentrich, J. M., Riess, O., Brunner, H. G., Brookes, A. J., Rath, A., Bonne, G., Gumus, G., Verloes, A., Hoogerbrugge, N., Evangelista, T., Harmuth, T., Swertz, M., Spalding, D., Hoischen, A., Beltran, S., Graessner, H., Nigro, V., Banfi, S., Torella, A., Piluso, G., Dürr, Alexandra, Lohmann, Katja, Kessler, Christoph, Wayand, Melanie, Wilke, Carlo, Traschuetz, Andreas, Schöls, Ludger, Hengel, Holger, Heutink, Peter, University of Tübingen, Radboud University Medical Center [Nijmegen], Newcastle Upon Tyne Hospitals NHS Foundation Trust, Barcelona Institute of Science and Technology (BIST), Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Leicester, Plateforme d'information et de services pour les maladies rares et les médicaments orphelins (Orphanet), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Broussais-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), EURORDIS-Rare Diseases Europe (Bureau de Paris), EURORDIS - Plateforme Maladies Rares [Paris], AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University Medical Center Groningen [Groningen] (UMCG), European Molecular Biology Laboratory [Hinxton], Universitat de Barcelona (UB), SOLVE-RD Consortium, Projekt DEAL, Unión Europea. Comisión Europea. H2020, European Reference Network for Rare Neurological Diseases (ERN-RND), Haack, T. B., Demidov, G., Sturm, M., Kessler, C., Wayand, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Heutink, P., Brunner, H., Scheffer, H., Steyaert, W., Sablauskas, K., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., te Paske, I., Janssen, E., de Boer, E., Steehouwer, M., Yaldiz, B., Kleefstra, T., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Specht, S., Clayton-Smith, J., Banka, S., Alexander, E., Jackson, A., Faivre, L., Thauvin, C., Denomme-Pichon, A. -S., Duffourd, Y., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Gut, I. G., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Garcia, C., Fernandez-Callejo, M., Hernandez, C., Pico, D., Paramonov, I., Lochmuller, H., Bros-Facer, V., Hanauer, M., Olry, A., Lagorce, D., Havrylenko, S., Izem, K., Rigour, F., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Allamand, V., Nelson, I., Yaou, R. B., Metay, C., Eymard, B., Cohen, E., Atalaia, A., Stojkovic, T., Macek, M., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Havlovicova, M., Kremlik, V., Parkinson, H., Keane, T., Senf, A., Robinson, P., Danis, D., Robert, G., Costa, A., Patch, C., Hanna, M., Houlden, H., Reilly, M., Vandrovcova, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., Van de Vondel, L., Beijer, D., de Jonghe, P., Musacchia, F., Ferlini, A., Selvatici, R., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., 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 Velde, J. K., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Drunat, S., Rooryck, C., Trimouille, A., Castello, R., Morleo, M., Pinelli, M., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., de la Rosa, F. J. A. G., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Renieri, A., Benetti, E., Balicza, P., Molnar, M. J., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., Macaya, A., Marce-Grau, A., Osorio, A. N., de Benito, D. N., Thompson, R., Polavarapu, K., Beeson, D., Cossins, J., Cruz, P. M. R., Hackman, P., Johari, M., Savarese, M., Udd, B., Horvath, R., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Schrock, E., Rump, A., Gestionnaire, HAL Sorbonne Université 5, Centre de Recherche en Myologie, Medicum, University of Helsinki, and Department of Medical and Clinical Genetics
Subjects: Computer science, Consensus Development Conferences as Topic, genetics [Rare Diseases], lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Diseases, Pan european, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Exome, Intersectoral Collaboration, Genetics (clinical), Exome sequencing, 0303 health sciences, 030305 genetics & heredity, Medical genetics, 1184 Genetics, developmental biology, physiology, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], 3. Good health, diagnosis [Rare Diseases], Europe, GENOME, Chemistry, New disease, Patient representatives, [SDV.MHEP.AHA] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], methods [Genetic Testing], MEDLINE, Socio-culturale, 03 medical and health sciences, Viewpoint, Rare Diseases, Exome Sequencing, Genetics, [SDV.MHEP.AHA]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Humans, ddc:610, Genetic Testing, Biology, 030304 developmental biology, genetics [Genetic Diseases, Inborn], Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Information Dissemination, Genetic Diseases, Inborn, Correction, Data science, diagnosis [Genetic Diseases, Inborn], Data sharing, methods [Exome Sequencing], 3111 Biomedicine, Human medicine, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], Rare disease
Abstract: For the first time in Europe hundreds of rare disease (RD) experts team up to actively share and jointly analyse existing patient's data. Solve-RD is a Horizon 2020-supported EU flagship project bringing together >300 clinicians, scientists, and patient representatives of 51 sites from 15 countries. Solve-RD is built upon a core group of four European Reference Networks (ERNs; ERN-ITHACA, ERN-RND, ERN-Euro NMD, ERN-GENTURIS) which annually see more than 270,000 RD patients with respective pathologies. The main ambition is to solve unsolved rare diseases for which a molecular cause is not yet known. This is achieved through an innovative clinical research environment that introduces novel ways to organise expertise and data. Two major approaches are being pursued (i) massive data re-analysis of >19,000 unsolved rare disease patients and (ii) novel combined -omics approaches. The minimum requirement to be eligible for the analysis activities is an inconclusive exome that can be shared with controlled access. The first preliminary data re-analysis has already diagnosed 255 cases form 8393 exomes/genome datasets. This unprecedented degree of collaboration focused on sharing of data and expertise shall identify many new disease genes and enable diagnosis of many so far undiagnosed patients from all over Europe. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. This research is supported (not financially) by four ERNs: (1) The ERN for Intellectual Disability, Telehealth and Congenital Anomalies (ERN-ITHACA)-Project ID No 869189; (2) The ERN on Rare Neurological Diseases (ERN-RND)-Project ID No 739510; (3) The ERN for Neuromuscular Diseases (ERN Euro-NMD)-Project ID No 870177; (4) The ERN on Genetic Tumour Risk Syndromes (ERN GENTURIS)-Project ID No 739547. The ERNs are co-funded by the European Union within the framework of the Third Health Programme. Open Access funding enabled and organized by Projekt DEAL. Sí
Published: 2021

34. Presupposti, sequenze e forme delle misure preventive personali su proposta dell'autorità giudiziaria

Author: Clelia Iasevoli, L. Luparia, F. Cassibba, M. Daniele, H. Belluta, A. Spinelli, N. Triggiani, T. Bene, A.Balsamo, C.Iasevoli, F. Consulich, S. Finocchiaro, V. Tondi, V. Mongolo, V. Maiello, E. Birritteri, M. Sestieri, C.Forte, S. Nuzzi, N. Santantonio, F. Siracusano, B. Galgani, P. Rivello, G. Canzio, E. Ciconte, I. Merenda, C. Visconti, G. Amarelli, S. De Blasis, E. Mezzetti, A. Gullo, I. Salvemme, L. Della Ragione, F. Cerqua, Enrico Mezzetti, Luca Luparia, and Iasevoli, Clelia
Subjects: sorveglianza speciale, misure preventive, presupposti
Abstract: Nelle varie accezioni di sicurezza sociale è possibile rintracciare una pregnante connotazione comune: essa ha a che fare con i contenuti limitativi di una situazione di libertà. Il concetto, ricostruito in termini normativi, come complesso di principi fondamentali, si presta a stimolare il consenso intorno alla legittimità della risposta legislativa richiesta dalla eccezionalità di taluni situazioni. In tal modo si perviene a giustificare anche l'uso del processo come mezzo di neutralizzazione della pericolosità di una persona in relazione a quella storicità del fatto che non assurge a tipicità offensiva e quindi che non costituisce reato. L'effetto è lo spostamento dell'asse di interesse dalla tutela del bene giuridico alla difesa dal tipo di autore, accentuando la contrapposizione tra tutela della collettività e diritti inviolabili dell'uomo.
Published: 2020

35. Digital generation of multivariate wind field processes

Author: I. Gullo, M. Di Paola, Di Paola, M., and Gullo, I.
Subjects: Stochastic process, Mechanical Engineering, Univariate, Aerospace Engineering, Spectral density, Ocean Engineering, Statistical and Nonlinear Physics, Condensed Matter Physics, Wind speed, Matrix (mathematics), Superposition principle, Nuclear Energy and Engineering, Autoregressive model, Calculus, Applied mathematics, Safety, Risk, Reliability and Quality, Eigenvalues and eigenvectors, Civil and Structural Engineering, Mathematics
Abstract: A very efficient procedure for the generation of multivariate wind velocity stochastic processes by wave superposition as well as autoregressive time series is proposed in this paper. The procedure starts by decomposing the wind velocity field into a summation of fully coherent independent vector processes using the frequency dependent eigenvectors of the Power Spectral Density matrix. It is shown that the application of the method allows to show some very interesting physical properties that allow to reduce drastically the computational effort. Moreover, using a standard finite element procedure for approximating the frequency dependent eigenvectors, the generation procedure requires the generation of a limited number of univariate fully coherent processes for describing the entire multivariate velocity processes independently of the number of components of the process.
Published: 2001

36. Fibrosis-related Transcriptome Unveils a Distinctive Remodelling Matrix Pattern in Penetrating Ileal Crohn's Disease.

Author: Tavares de Sousa H, Ferreira M, Gullo I, Rocha AM, Pedro A, Leitão D, Oliveira C, Carneiro F, and Magro F
Subjects: Humans, Male, Female, Adult, Middle Aged, Constriction, Pathologic genetics, Young Adult, Gene Expression Profiling methods, Crohn Disease genetics, Crohn Disease pathology, Crohn Disease metabolism, Fibrosis genetics, Transcriptome, Ileum pathology, Ileum metabolism, Ileum surgery
Abstract: Background and Aims: Stricturing [B2] and penetrating [B3] ileal Crohn's disease have been reported to present similar levels of histopathological transmural fibrosis. This study aimed to compare the fibrosis-related transcriptomic profiles of penetrating and stricturing ileal Crohn's disease., Methods: Using Nanostring technology and comparative bioinformatics, we analysed the expression of 787 fibrosis-related genes in 36 ileal surgical specimens, 12 B2 and 24 B3, the latter including 12 cases with associated stricture[s] [B3s] and 12 without [B3o]. Quality control of extracted RNA was performed according to Nanostring parameters and principal component analysis for the distribution analysis. For the selection of the differentially expressed genes, a p-adjusted <0.05 and fold change ≤-1.5 or ≥1.5 were adopted. Quantitative polymerase chain reaction (qPCR) and immunohistochemistry analyses were used to validate selected differentially expressed genes., Results: We included 34 patients with B2 and B3 phenotypes, balanced for age at diagnosis, age at surgery, gender, Crohn's disease localisation, perianal disease, and therapy. Inflammation and fibrosis histopathological scoring were similar in all cases. B2 and B3 groups showed a very good clustering regarding 30 significantly differentially expressed genes, all being remarkably upregulated in B3. More than half of these genes were involved in Crohn's disease fibrogenesis, and eight differentially expressed genes were so in other organs. The most significantly active biological processes and pathways in penetrating disease were response to TGFβ and matrix organisation and degradation, as validated by immunohistochemistry., Conclusions: Despite the histopathological similarities in fibrosis between stricturing and penetrating ileal Crohn's disease, their fibrosis-related transcriptomic profiles are distinct. Penetrating disease exhibits a distinctive transcriptomic landscape related to enhanced matrix remodelling., (© The Author(s) 2024. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
Published: 2024
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37. Higher frequency of gastric neoplasia in advanced chronic liver disease patients: Impact of screening endoscopy in an intermediate-high risk country.

Author: Morais R, Moreira J, Gaspar R, Santos-Antunes J, Marques M, Coelho R, Alves R, Ferreira-Silva J, Dias E, Pereira P, Lopes S, Cardoso H, Sousa-Pinto B, Faria-Ramos I, Gullo I, Carneiro F, Liberal R, and Macedo G
Abstract: Background: The Baveno VII guidelines were proposed to identify which patients could safely avoid screening esophagogastroduodenoscopy (EGD) for gastroesophageal varices. We aimed to evaluate the frequency of gastric neoplasia in compensated advanced chronic liver disease (cACLD) patients who underwent EGD for screening of gastroesophageal varices (GOEV) compared to a healthy population., Methods: Retrospective study that enrolled all cACLD patients who underwent EGD for GOEV screening (January 2008-June 2018) in a tertiary reference center. cACLD patients were compared with asymptomatic healthy individuals who underwent EGD in a private hospital setting (April 2017-March 2018)., Results: We evaluated 1845 patients (481 cACLD patients, 1364 healthy individuals). A significantly higher frequency of gastric neoplasia was observed in patients with cACLD compared to healthy individuals (4.0% vs. 1.0 %; p < 0.001). Rare histopathological subtypes (WHO Classification) accounted for 28.7 % of gastric carcinoma cases in the cACLD cohort. Seven cases of gastric neoplasia (36.8 % of gastric neoplasia cases in the cACLD patients) were diagnosed in patients who, according to the Baveno VII criteria, would have not been submitted to EGD., Conclusion: We found an increased frequency of gastric neoplasia in patients with cACLD in comparison with healthy individuals. In countries with intermediate-high risk for GC, continuing to perform EGD could be beneficial., Competing Interests: Conflict of interest None., (Copyright © 2024 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.)
Published: 2024
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38. Underwater Endoscopic Mucosal Resection Vs Conventional Endoscopic Mucosal Resection for Superficial Nonampullary Duodenal Epithelial Tumors in the Western Setting.

Author: Morais R, Amorim J, Medas R, Sousa-Pinto B, Santos-Antunes J, Legros R, Albouys J, Moll F, Marques M, Vilas-Boas F, Rodrigues-Pinto E, Gullo I, Carneiro F, Soares EG, Amaro P, Mesquita P, Rodrigues J, Andrisani G, Sferrazza S, Archer S, Kuttner-Magalhães R, Manzano F, de Santiago ER, Rimondi A, Murino A, Despott E, Pioche M, Jacques J, and Macedo G
Abstract: Background & Aims: Conventional endoscopic mucosal resection (C-EMR) is established as the primary treatment modality for superficial nonampullary duodenal epithelial tumors (SNADETs), but recently underwater endoscopic mucosal resection (U-EMR) has emerged as a potential alternative. The majority of previous studies focused on Asian populations and small lesions (≤20 mm). We aimed to compare the efficacy and outcomes of U-EMR vs C-EMR for SNADETs in a Western setting., Methods: This was a retrospective multinational study from 10 European centers that performed both C-EMR and U-EMR between January 2013 and July 2023. The main outcomes were the technical success, procedure-related adverse events (AEs), and the residual/recurrent adenoma (RRA) rate, evaluated on a per-lesion basis. We assessed the association between the type of endoscopic mucosal resection and the occurrence of AEs or RRAs using mixed-effects logistic regression models (propensity scores). Sensitivity analyses were performed for lesions ≤20 mm or >20 mm., Results: A total of 290 SNADETs submitted to endoscopic resection during the study period met the inclusion criteria and were analyzed (C-EMR: n = 201, 69.3%; U-EMR: n = 89, 30.7%). The overall technical success rate was 95.5% and comparable between groups. In logistic regression models, compared with U-EMR, C-EMR was associated with a significantly higher frequency of overall delayed AEs (odds ratio [OR], 4.95; 95% CI, 2.87-8.53), postprocedural bleeding (OR, 7.92; 95% CI, 3.95-15.89), and RRAs (OR, 3.66; 95% CI, 2.49-5.37). Sensitivity analyses confirmed these results when solely considering either small (≤20 mm) or large (>20 mm) lesions., Conclusions: Compared with C-EMR, U-EMR was associated with a lower rate of overall AEs and RRAs, regardless of lesion size. Our results confirm the possible role of U-EMR as an effective and safe technique in the management of SNADETs., (Copyright © 2024 AGA Institute. Published by Elsevier Inc. All rights reserved.)
Published: 2024
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39. HER2 and PD-L1 Expression in Gastric and Gastroesophageal Junction Cancer: Insights for Combinatorial Targeting Approaches.

Author: Freitas MB, Gullo I, Leitão D, Águas L, Oliveira C, Polónia A, Gomes J, Carneiro F, Reis CA, and Duarte HO
Abstract: Gastric and gastroesophageal junction adenocarcinomas (GA/GEJA) are associated with a poor prognosis, primarily due to late disease diagnosis. Human Epidermal Growth Factor Receptor 2 (HER2) overexpression and programmed death-ligand 1 (PD-L1) expression are important biomarkers for treatment selection in locally advanced unresectable and metastatic GA/GEJA, and there is increasing interest in their role in earlier stages of disease. In this study, we aimed to evaluate HER2 and PD-L1 expression in a curative-intent GA/GEJA cohort to describe their expression patterns and analyze the association between HER2 expression and clinicopathological features. HER2 expression was evaluated in surgical and endoscopic submucosal dissection tumor samples, and PD-L1 was evaluated in HER2-positive cases. The clinical cohort included 107 patients, with 8.4% testing positive for HER2 (seven of whom also exhibited a PD-L1 combined positive score of ≥1. HER2 status was not significantly associated with survival outcomes. A pathologist-guided, region-specific analysis revealed that PD-L1 expression rarely overlaps with HER2-positive tumor areas. While the therapeutic implications of these observations remain unknown, these findings suggest that combination strategies targeting HER2 and PD-L1 might be directed toward distinct tumor subclones. The herein disclosed region-specific biomarker expression patterns may have important therapeutic and prognostic impacts, warranting further evaluation., Competing Interests: The authors declare no conflicts of interest.
Published: 2024
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40. Morphologic Heterogeneity of Carcinoma with Signet Ring Cell Features at Different Primary Sites.

Author: Dahoud W, Gullo I, Imam R, and Tang LH
Subjects: Humans, Female, Mucins metabolism, Stomach Neoplasms pathology, Breast Neoplasms pathology, Male, Neoplasms, Unknown Primary pathology, Adenocarcinoma pathology, Lung Neoplasms pathology, Appendiceal Neoplasms pathology, Carcinoma, Signet Ring Cell pathology
Abstract: Introduction: Signet ring cells (SRCs) may be observed in carcinomas from multiple primary sites. Elucidating unknown primaries from metastases with SRCs represents a diagnostic challenge. This study examined morphologic characteristics of adenocarcinomas with SRCs from stablished primary sites and described objective features, which can aid in identifying the site of origin., Methods: The series encompasses 257 cases of adenocarcinomas with SRCs from gastroesophageal junction (GEJ, n = 38), stomach (n = 48), pancreatobiliary system (n = 16), colorectum (n = 40), appendix (n = 32), breast (n = 41), and lung (n = 42). H&E sections were examined and scored using architectural and cytologic criteria. Morphometric analysis was performed using QuPath software., Results: Extracellular mucin was more abundant in GEJ, colorectal, and appendiceal carcinomas. Poorly cohesive morphology was the most frequent pattern in gastric and breast carcinomas. The cytoplasmic mucin/vacuole was predominantly clear and targetoid in breast carcinomas. Breast and gastric carcinomas showed the highest nuclear to cytoplasmic (N/C) ratio, whereas appendiceal carcinoma the lowest., Conclusion: Morphological evaluation (extracellular mucin, architectural patterns, and the nature of cytoplasmic mucin/vacuole) represents an important step to determine the cancer site of origin in adenocarcinomas with SRCs and guides further ancillary studies. Cytological morphometry may help further refine morphological criteria and facilitate the construction of digital-pathology algorithms., (© 2023 S. Karger AG, Basel.)
Published: 2024
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41. Gastric Polyps in Familial Adenomatous Polyposis Portuguese Patients: The First Western Cohort with Asian Features.

Author: Baptista D, Fernandes M, Garrido M, Sousa F, Morais R, Garcia-Pelaez J, Silva R, Leitão D, Baptista M, Barbosa J, Carneiro F, and Gullo I
Subjects: Humans, Female, Male, Adult, Portugal epidemiology, Retrospective Studies, Middle Aged, Prevalence, Gastric Mucosa pathology, Helicobacter Infections complications, Helicobacter Infections epidemiology, Helicobacter Infections pathology, Helicobacter pylori, Young Adult, Gastritis, Atrophic pathology, Gastritis, Atrophic epidemiology, Adolescent, Aged, Adenoma pathology, Adenoma epidemiology, Polyps pathology, Polyps epidemiology, Metaplasia, Adenomatous Polyps, Adenomatous Polyposis Coli pathology, Adenomatous Polyposis Coli epidemiology, Adenomatous Polyposis Coli complications, Stomach Neoplasms pathology, Stomach Neoplasms epidemiology
Abstract: Introduction: Chronic atrophic gastritis may contribute to gastric polyps (GP) phenotype in familial adenomatous polyposis (FAP). Considering the high prevalence of Helicobacter pylori (HP) infection in Portugal, we aim to characterize GP in a series of Portuguese patients., Methods: In a retrospectively selected series of 53 FAP patients, clinical data and histopathological features of GP and background gastric mucosa were studied. SPSS (27.0) was used for statistical analysis., Results: Thirteen patients (24.5%) developed fundic gland polyps (FGP), seven (13.2%) gastric adenomas (GA), and ten (18.9%) both FGP and GA. Out of 100 GP, four were hyperplastic polyps, 58 FGP (24 with dysplasia), 35 intestinal-type GA (intGA), and three foveolar-type GA (fovGA). IntGA were larger (60% >7 mm, p = 0.03), occurred predominantly in the distal stomach (66.7%, p = 0.024), in patients harboring gastric intestinal metaplasia (IM) (86.7%, p < 0.001), and duodenal adenomas (86.7%, p < 0.001)., Conclusion: This is the first Western series showing high prevalence of intGA in FAP patients, comparable to Asian cohorts. HP infection and chronic atrophic gastritis/intestinal metaplasia are likely responsible for this difference, with risk of neoplastic transformation and management implications. Biopsy/excision of GP >7 mm in the distal stomach and in patients harboring gastric intestinal metaplasia/duodenal adenomas should be considered., (© 2023 S. Karger AG, Basel.)
Published: 2024
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42. Predicting residual neoplasia after a non-curative gastric ESD: validation and modification of the eCura system in the Western setting: the W-eCura score.

Author: Morais R, Libanio D, Dinis Ribeiro M, Ferreira A, Barreiro P, Bourke MJ, Gupta S, Amaro P, Küttner Magalhães R, Cecinato P, Boal Carvalho P, Pinho R, Rodríguez de Santiago E, Sferrazza S, Lemmers A, Figueiredo M, Pioche M, Gallego F, Albéniz E, Ramos Zabala F, Uchima H, Berr F, Wagner A, Marques M, Pimentel-Nunes P, Gonçalves M, Mascarenhas A, Soares EG, Xavier S, Faria-Ramos I, Sousa-Pinto B, Gullo I, Carneiro F, Macedo G, and Santos-Antunes J
Subjects: Humans, Retrospective Studies, Risk Factors, Gastrectomy methods, Endoscopy, Gastrointestinal, Gastric Mucosa surgery, Gastric Mucosa pathology, Endoscopic Mucosal Resection, Stomach Neoplasms surgery, Stomach Neoplasms pathology
Abstract: Objective: To evaluate the risk factors for lymph node metastasis (LNM) after a non-curative (NC) gastric endoscopic submucosal dissection (ESD) and to validate and eventually refine the eCura scoring system in the Western setting. Also, to assess the rate and risk factors for parietal residual disease., Design: Retrospective multicentre multinational study of prospectively collected registries from 19 Western centres. Patients who had been submitted to surgery or had at least one follow-up endoscopy were included. The eCura system was applied to assess its accuracy in the Western setting, and a modified version was created according to the results (W-eCura score). The discriminative capacities of the eCura and W-eCura scores to predict LNM were assessed and compared., Results: A total of 314 NC gastric ESDs were analysed (72% high-risk resection (HRR); 28% local-risk resection). Among HRR patients submitted to surgery, 25% had parietal disease and 15% had LNM in the surgical specimen. The risk of LNM was significantly different across the eCura groups (areas under the receiver operating characteristic curve (AUC-ROC) of 0.900 (95% CI 0.852 to 0.949)). The AUC-ROC of the W-eCura for LNM (0.916, 95% CI 0.870 to 0.961; p=0.012) was significantly higher compared with the original eCura. Positive vertical margin, lymphatic invasion and younger age were associated with a higher risk of parietal residual lesion in the surgical specimen., Conclusion: The eCura scoring system may be applied in Western countries to stratify the risk of LNM after a gastric HRR. A new score is proposed that may further decrease the number of unnecessary surgeries., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)
Published: 2023
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43. Role of Endoscopic Biopsies and Morphologic Features in Predicting Microsatellite Instability Status in Gastric Cancer: A Multicenter Comparative Study of Endoscopic Biopsies and Surgical Specimens.

Author: Silva JR, Mascarenhas-Lemos L, Neto do Nascimento C, Sousa Marques D, Wen X, Pinho L, Maio R, Pontes P, Cirnes L, Cravo M, Carneiro F, and Gullo I
Subjects: Humans, Microsatellite Instability, Retrospective Studies, Immunohistochemistry, Biopsy, DNA Mismatch Repair, Microsatellite Repeats, Stomach Neoplasms genetics, Stomach Neoplasms surgery, Stomach Neoplasms metabolism, Colorectal Neoplasms pathology
Abstract: Evaluation of mismatch repair (MMR) protein and microsatellite instability (MSI) status plays a pivotal role in the management of gastric cancer (GC) patients. In this study, we aimed to evaluate the accuracy of gastric endoscopic biopsies (EBs) in predicting MMR/MSI status and to uncover histopathologic features associated with MSI. A multicentric series of 140 GCs was collected retrospectively, in which EB and matched surgical specimens (SSs) were available. Laurén and WHO classifications were applied and detailed morphologic characterization was performed. EB/SS were analyzed by immunohistochemistry (IHC) for MMR status and by multiplex polymerase chain reaction (mPCR) for MSI status. IHC allowed accurate evaluation of MMR status in EB (sensitivity: 97.3%; specificity: 98.0%) and high concordance rates between EB and SS (Cohen κ=94.5%). By contrast, mPCR (Idylla MSI Test) showed lower sensitivity in evaluating MSI status (91.3% vs. 97.3%), while maintaining maximal specificity (100.0%). These results suggest a role of IHC as a screening method for MMR status in EB and the use of mPCR as a confirmatory test. Although Laurén/WHO classifications were not able to discriminate GC cases with MSI, we identified specific histopathologic features that are significantly associated with MMR/MSI status in GC, despite the morphologic heterogeneity of GC cases harboring this molecular phenotype. In SS, these features included the presence of mucinous and/or solid components ( P =0.034 and <0.001) and the presence of neutrophil-rich stroma, distant from tumor ulceration/perforation ( P <0.001). In EB, both solid areas and extracellular mucin lakes were also discriminating features for the identification of MSI-high cases ( P =0.002 and 0.045)., Competing Interests: Conflicts of Interest and Source of Funding: Partially co-financed by Hospital da Luz under the initiative “Luz Investigação” in the context of the Group GENIUS (Reference LH.INV.F2019015). Part of the Idylla reagents have been provided free of charge by Biocartis. The funding source did not have any influence on the design, conduction, analysis, and interpretation of data and report of the results for this study. The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)
Published: 2023
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44. 3D Chromatin Architecture Re-Wiring at the CDH3/CDH1 Loci Contributes to E-Cadherin to P-Cadherin Expression Switch in Gastric Cancer.

Author: São José C, Pereira C, Ferreira M, André A, Osório H, Gullo I, Carneiro F, and Oliveira C
Abstract: Cadherins are cell-cell adhesion molecules, fundamental for cell architecture and polarity. E-cadherin to P-cadherin switch can rescue adherens junctions in epithelial tumours. Herein, we disclose a mechanism for E-cadherin to P-cadherin switch in gastric cancers. CDH1 and CDH3 mRNA expression was obtained from 42 gastric tumours' RNA-seq data. CRISPR-Cas9 was used to knock out CDH1 and a putative regulatory element. CDH1 -depleted and parental cells were submitted to proteomics and enrichment GO terms analysis; ATAC-seq/4C-seq with a CDH1 promoter viewpoint to assess chromatin accessibility and conformation; and RT-PCR/flow cytometry to assess CDH1 /E-cadherin and CDH3 /P-cadherin expression. In 42% of gastric tumours analysed, CDH1 to CDH3 switch was observed. CDH1 knockout triggered CDH1 /E-cadherin complete loss and CDH3 /P-cadherin expression increase at plasma membrane. This switch, likely rescuing adherens junctions, increased cell migration/proliferation, commonly observed in aggressive tumours. E- to P-cadherin switch accompanied increased CDH1 promoter interactions with CDH3 -eQTL, absent in normal stomach and parental cells. CDH3 -eQTL deletion promotes CDH3 / CDH1 reduced expression. These data provide evidence that loss of CDH1 /E-cadherin expression alters the CDH3 locus chromatin conformation, allowing a CDH1 promoter interaction with a CDH3 -eQTL, and promoting CDH3 /P-cadherin expression. These data highlight a novel mechanism triggering E- to P-cadherin switch in gastric cancer.
Published: 2023
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45. DOES NEOADJUVANT CHEMORADIOTHERAPY FOR ESOPHAGEAL AND GASTROESOPHAGEAL JUNCTION CANCER PATIENTS AFFECT POSTOPERATIVE OUTCOMES? A STUDY USING THE BECKER TUMOR REGRESSION GRADE SYSTEM AND LYMPH NODE REGRESSION.

Author: Rosário MIVD, Barbosa JP, Gullo I, and Barbosa J
Subjects: Humans, Retrospective Studies, Esophagogastric Junction, Lymph Nodes, Neoadjuvant Therapy, Adenocarcinoma therapy
Abstract: Background: The effect of neoadjuvant chemoradiotherapy (nCRT) in patients with locally advanced esophageal cancer can be determined by assessing the Becker tumor regression grade in the primary tumor, as well as in lymph nodes., Aims: The aim of this study was to investigate the anatomopathological changes caused by neoadjuvant chemoradiotherapy and their impact on clinical parameters. Specifically, we analyzed the Becker tumor regression grade, lymph node status, and regression changes and evaluated their association with the Clavien-Dindo classification of surgical complications and overall patient survival., Methods: This is a retrospective and observational study including 139 patients diagnosed with adenocarcinoma or squamous cell carcinoma of the esophagus and treated with either neoadjuvant chemoradiotherapy followed by surgery or surgery alone. For the 94 patients who underwent neoadjuvant chemoradiotherapy, we evaluated tumor regression by Becker tumor regression grade in primary tumors. We also analyzed lymph node status and regression changes on lymph nodes with or without metastases. Overall survival analysis was performed using Kaplan-Meier curves., Results: Becker tumor regression grade is associated with lower lymphatic permeation (p<0.01) and vascular invasion (p<0.001), but not with lymph node regression rate (p=0.10). Clavien-Dindo classification was associated neither with lymph node regression rate (odds ratio=0.784, p=0.795) nor with tumor regression grade (p=0.68). Patients who presented with lymphatic permeation and vascular invasion had statistically significantly lower median survival (17 vs. 30 months, p=0.006 for lymphatic permeation, and 14 vs. 29 months, p=0.024 for vascular invasion)., Conclusion: In our series, we were unable to demonstrate an association between Becker tumor regression grade and lymph node regression rate with any postoperative complications. Patients with lower lymphatic permeation and vascular invasion have higher overall survival, correlating with a better response in the Becker tumor regression grade system.
Published: 2023
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46. Fibromuscular Expansion in Crohn's Disease Ileal Strictures: An Open Issue.

Author: de Sousa HT, Gullo I, and Magro F
Subjects: Humans, Constriction, Pathologic, Anastomosis, Surgical, Crohn Disease complications, Crohn Disease diagnosis, Intestinal Obstruction diagnosis, Intestinal Obstruction etiology, Intestinal Obstruction surgery
Published: 2023
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47. A practical approach for PD-L1 evaluation in gastroesophageal cancer.

Author: Angerilli V, Fassan M, Parente P, Gullo I, Campora M, Rossi C, Sacramento ML, Pennelli G, Vanoli A, Grillo F, and Mastracci L
Subjects: Humans, B7-H1 Antigen, Biomarkers, Tumor, Esophageal Neoplasms diagnosis, Esophageal Neoplasms pathology, Esophageal Squamous Cell Carcinoma, Adenocarcinoma diagnosis, Adenocarcinoma pathology, Stomach Neoplasms diagnosis, Stomach Neoplasms pathology
Abstract: PD-L1 is an established predictive immunohistochemical biomarker of response to immune checkpoint inhibitors. At present, PD-L1 is routinely assessed on biopsy samples of advanced gastroesophageal cancer patients before initiating first-line treatment. However, PD-L1 is still a suboptimal biomarker, due to changing cut-off values and scoring systems, interobserver and interlaboratory variability., This practical illustrated review discusses the range of staining patterns of PD-L1 and the potential pitfalls and challenges that can be encountered when evaluating PD-L1, focusing on gastric and gastroesophageal adenocarcinoma (G/GEA) and esophageal squamous cell carcinoma (ESCC)., (Copyright © 2022 Società Italiana di Anatomia Patologica e Citopatologia Diagnostica, Divisione Italiana della International Academy of Pathology.)
Published: 2023
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48. Acute gastrointestinal graft-versus-host disease with cytomegalovirus and Epstein-Barr virus superinfection in a patient with COVID-19.

Author: Dias E, Marques M, Lopes S, Gullo I, Bastos J, and Macedo G
Subjects: Female, Humans, Middle Aged, Herpesvirus 4, Human genetics, Cytomegalovirus genetics, RNA, Viral therapeutic use, SARS-CoV-2, Epstein-Barr Virus Infections complications, Epstein-Barr Virus Infections diagnosis, Superinfection complications, COVID-19 complications, Cytomegalovirus Infections complications, Cytomegalovirus Infections drug therapy, Graft vs Host Disease complications
Abstract: A 60-year-old female was diagnosed with acute myeloid leukemia. After initial remission with chemotherapy, she relapsed and underwent allogeneic hematopoietic stem cell transplantation (HSCT). Two months later, she presented to emergency department with watery diarrhea, abdominal pain and fever. She also tested positive for SARS-CoV2 on nasopharyngeal swab by polymerase chain reaction (PCR) and both cytomegalovirus (CMV) and Epstein-Barr virus (EBV) were detected in peripheral blood. Flexible sigmoidoscopy showed diffuse edema, erythema and loss of vascular pattern with interspersed segments of mucosal denudation and exudate and bBiopsies revealed epithelial cell apoptosis, diffuse crypt atrophy and dropout, with ulceration and both CMV and EBV were detected in colon mucosa, consistent with acute severe gastrointestinal graft-versus-host disease complicated by CMV and EBV superinfection. Despite starting therapy with methylprednisolone, ganciclovir and rituximab,she presented unfavorable evolution and died after 5 weeks.
Published: 2023
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49. Primary small bowel follicular lymphoma: the role of balloon-assisted enteroscopy in diagnosis and follow-up.

Author: Dias E, Andrade P, Cardoso H, Gullo I, Fonseca E, and Macedo G
Subjects: Male, Humans, Adult, Follow-Up Studies, Ileum pathology, Double-Balloon Enteroscopy methods, Lymphoma, Follicular diagnostic imaging, Lymphoma, Follicular therapy, Capsule Endoscopy
Abstract: An asymptomatic 38-year-old male with no significant previous medical history performed routine laboratory studies that revealed iron-deficiency anemia. Esophagogastroduodenoscopy and colonoscopy were unremarkable and he undergone videocapsule endoscopy that revealed multiple small polyps along jejunum and ileum. Double-balloon enteroscopy confirmed the presence of scattered small whitish nodules and small polyps carpeting segments of jejunal mucosal and sometimes forming conglomerates with a nodular appearance. Histopathological examination showed lamina propria expansion by neoplastic follicles, predominantly composed by small lymphoid cells that, by immunohistochemistry, showed expression of CD20, CD10 and bcl-2. Computed tomography scan of abdomen and pelvis did not reveal systemic involvement, consistent with primary small bowel follicular lymphoma. Chemotherapy was started and, at reevaluation enteroscopy, although nodular jejunal segments persisted, biopsies did not show involvement by lymphoproliferative disease, which was interpreted as complete remission. Periodic clinical and biochemical evaluation and annual enteroscopic surveillance was maintained and, after three years, local recurrence of low-grade follicular lymphoma was detected. As previously, there was no evidence of systemic involvement and the decision was to maintain close surveillance. After one year, the patient remains asymptomatic and without evidence of disease progression. This case illustrates the essential role of balloon-assisted enteroscopy for diagnosis and surveillance of primary small bowel follicular lymphoma.
Published: 2023
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50. Performance of Immunohistochemical and Molecular Methods in Detecting Microsatellite Instability in Gastric Cancer: A Multicenter Study.

Author: Sousa Marques D, Gullo I, Mascarenhas-Lemos L, Silva JR, Neto do Nascimento C, Pontes P, Pinho L, Cirnes L, Wen X, Cravo M, and Carneiro F
Subjects: Humans, Microsatellite Instability, Biomarkers, Tumor analysis, Immunohistochemistry, Microsatellite Repeats, Stomach Neoplasms diagnosis, Stomach Neoplasms genetics, Colorectal Neoplasms genetics
Abstract: Introduction: Microsatellite instability (MSI) is an important prognostic molecular biomarker for gastric cancer (GC). MSI status may be detected by immunohistochemistry (IHC) for mismatch repair (MMR) proteins and polymerase chain reaction (PCR). Idylla™ MSI assay has not been validated for GC but may prove to be a valid alternative., Methods: In a series of 140 GC cases, MSI status was evaluated by IHC for MLH1, PMS2, MSH2, and MSH6; gold-standard pentaplex PCR panel (PPP) (BAT-25, BAT-26, NR-21, NR-24, and NR-27); and Idylla. Statistical analysis was performed using SPSS 27.0., Results: PPP identified 102 microsatellite stable (MSS) cases and 38 MSI-high cases. Only 3 cases showed discordant results. Compared with PPP, the sensitivity was 100% for IHC and 94.7% for Idylla. Specificity was 99% for IHC and 100% for Idylla. MLH1 IHC alone showed sensitivity and specificity of 97.4% and 98.0%, respectively. IHC identified three indeterminate cases; all were MSS according to PPP and Idylla., Conclusion: IHC for MMR proteins represents an optimal screening tool for MSI status in GC. If resources are limited, isolated MLH1 evaluation may constitute a valuable option for preliminary screening. Idylla may help detect rare MSS cases with MMR-loss and define MSI status in indeterminate cases., (© 2023 S. Karger AG, Basel.)
Published: 2023
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