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1. Combined loss of CDH1 and downstream regulatory sequences drive early-onset diffuse gastric cancer and increase penetrance of hereditary diffuse gastric cancer

Author

São José, Celina, Garcia-Pelaez, José, Ferreira, Marta, Arrieta, Oscar, André, Ana, Martins, Nelson, Solís, Samantha, Martínez-Benítez, Braulio, Ordóñez-Sánchez, María Luisa, Rodríguez-Torres, Maribel, Sommer, Anna K., te Paske, Iris B. A. W., Caldas, Carlos, Tischkowitz, Marc, Tusié, Maria Teresa, Hoogerbrugge, Nicoline, Demidov, German, de Voer, Richarda M., Laurie, Steve, and Oliveira, Carla

Published
2023
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2. Correction: Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples

Author

Wijngaard, Robin, Demidov, German, O’Gorman, Luke, Corominas-Galbany, Jordi, Yaldiz, Burcu, Steyaert, Wouter, de Boer, Elke, Vissers, Lisenka E. L. M., Kamsteeg, Erik-Jan, Pfundt, Rolph, Swinkels, Hilde, den Ouden, Amber, te Paske, Iris B. A. W., de Voer, Richarda M., Faivre, Laurence, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Vitobello, Antonio, Chevarin, Martin, Straub, Volker, Töpf, Ana, van der Kooi, Anneke J., Magrinelli, Francesca, Rocca, Clarissa, Hanna, Michael G., Vandrovcova, Jana, Ossowski, Stephan, Laurie, Steven, and Gilissen, Christian

Published
2024
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3. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Denommé-Pichon, Anne-Sophie, Matalonga, Leslie, de Boer, Elke, Jackson, Adam, Benetti, Elisa, Banka, Siddharth, Bruel, Ange-Line, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Duffourd, Yannis, Ellwanger, Kornelia, Fallerini, Chiara, Gilissen, Christian, Graessner, Holm, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jean-Marçais, Nolwenn, Kleefstra, Tjitske, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Pizzi, Simone, Posada, Manuel, Radio, Francesca Clementina, Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Safraou, Hana, Schwarz, Martin, Tartaglia, Marco, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, Trimouille, Aurélien, Votypka, Pavel, de Vries, Bert B. A., Willemsen, Marjolein H., Zurek, Birte, Verloes, Alain, Philippe, Christophe, Abbott, Kristin M., Faivre, Laurence, Kerstjens, Mieke, Martín, Estrella López, Macek Jr., Milan, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Radio, Francesca C., Riess, Olaf, Agathe, Jean-Madeleine De Sainte, Santen, Gijs W. E., Thauvin, Christel, Torella, Annalaura, Vissers, Lisenka, Vitobello, Antonio, Zguro, Kristina, Boer, Elke De, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B. A. W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, `t Hoen, Peter A. C., Vissers, Lisenka E. L. M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris Te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Li\vsková, Petra, Dole\vzalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, 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 Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A. L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, Alembik, Yves, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Denommé-Pichon, Anne-Sophie, Matalonga, Leslie, de Boer, Elke, Jackson, Adam, Benetti, Elisa, Banka, Siddharth, Bruel, Ange-Line, Ciolfi, Andrea, Clayton-Smith, Jill, Dallapiccola, Bruno, Duffourd, Yannis, Ellwanger, Kornelia, Fallerini, Chiara, Gilissen, Christian, Graessner, Holm, Haack, Tobias B., Havlovicova, Marketa, Hoischen, Alexander, Jean-Marçais, Nolwenn, Kleefstra, Tjitske, López-Martín, Estrella, Macek, Milan, Mencarelli, Maria Antonietta, Moutton, Sébastien, Pfundt, Rolph, Pizzi, Simone, Posada, Manuel, Radio, Francesca Clementina, Renieri, Alessandra, Rooryck, Caroline, Ryba, Lukas, Safraou, Hana, Schwarz, Martin, Tartaglia, Marco, Thauvin-Robinet, Christel, Thevenon, Julien, Tran Mau-Them, Frédéric, Trimouille, Aurélien, Votypka, Pavel, de Vries, Bert B. A., Willemsen, Marjolein H., Zurek, Birte, Verloes, Alain, Philippe, Christophe, Abbott, Kristin M., Faivre, Laurence, Kerstjens, Mieke, Martín, Estrella López, Macek Jr., Milan, Maystadt, Isabelle, Morleo, Manuela, Nigro, Vicenzo, Pinelli, Michele, Radio, Francesca C., Riess, Olaf, Agathe, Jean-Madeleine De Sainte, Santen, Gijs W. E., Thauvin, Christel, Torella, Annalaura, Vissers, Lisenka, Vitobello, Antonio, Zguro, Kristina, Boer, Elke De, Cohen, Enzo, Danis, Daniel, Gao, Fei, Horvath, Rita, Johari, Mridul, Johanson, Lennart, Li, Shuang, Morsy, Heba, Nelson, Isabelle, Paramonov, Ida, te Paske, Iris B. A. W., Robinson, Peter, Savarese, Marco, Steyaert, Wouter, Töpf, Ana, van der Velde, Joeri K., Vandrovcova, Jana, Ossowski, Stephan, Demidov, German, Sturm, Marc, Schulze-Hentrich, Julia M., Schüle, Rebecca, Xu, Jishu, Kessler, Christoph, Wayand, Melanie, Synofzik, Matthis, Wilke, Carlo, Traschütz, Andreas, Schöls, Ludger, Hengel, Holger, Lerche, Holger, Kegele, Josua, Heutink, Peter, Brunner, Han, Scheffer, Hans, Hoogerbrugge, Nicoline, `t Hoen, Peter A. C., Vissers, Lisenka E. L. M., Sablauskas, Karolis, de Voer, Richarda M., Kamsteeg, Erik-Jan, van de Warrenburg, Bart, van Os, Nienke, Paske, Iris Te, Janssen, Erik, Steehouwer, Marloes, Yaldiz, Burcu, Brookes, Anthony J., Veal, Colin, Gibson, Spencer, Maddi, Vatsalya, Mehtarizadeh, Mehdi, Riaz, Umar, Warren, Greg, Dizjikan, Farid Yavari, Shorter, Thomas, Straub, Volker, Bettolo, Chiara Marini, Manera, Jordi Diaz, Hambleton, Sophie, Engelhardt, Karin, Alexander, Elizabeth, Peyron, Christine, Pélissier, Aurore, Beltran, Sergi, Gut, Ivo Glynne, Laurie, Steven, Piscia, Davide, Papakonstantinou, Anastasios, Bullich, Gemma, Corvo, Alberto, Fernandez-Callejo, Marcos, Hernández, Carles, Picó, Daniel, Lochmüller, Hanns, Gumus, Gulcin, Bros-Facer, Virginie, Rath, Ana, Hanauer, Marc, Lagorce, David, Hongnat, Oscar, Chahdil, Maroua, Lebreton, Emeline, Stevanin, Giovanni, Durr, Alexandra, Davoine, Claire-Sophie, Guillot-Noel, Léna, Heinzmann, Anna, Coarelli, Giulia, Bonne, Gisèle, Evangelista, Teresinha, Allamand, Valérie, Ben Yaou, Rabah, Metay, Corinne, Eymard, Bruno, Atalaia, Antonio, Stojkovic, Tanya, Turnovec, Marek, Thomasová, Dana, Kremliková, Radka Pourová, Franková, Vera, Havlovicová, Markéta, Li\vsková, Petra, Dole\vzalová, Pavla, Parkinson, Helen, Keane, Thomas, Freeberg, Mallory, Thomas, Coline, Spalding, Dylan, Robert, Glenn, Costa, Alessia, Patch, Christine, Hanna, Mike, Houlden, Henry, Reilly, Mary, Efthymiou, Stephanie, Cali, Elisa, Magrinelli, Francesca, Sisodiya, Sanjay M., Rohrer, Jonathan, Muntoni, Francesco, Zaharieva, Irina, Sarkozy, Anna, Timmerman, Vincent, Baets, Jonathan, de Vries, Geert, De Winter, Jonathan, Beijer, Danique, de Jonghe, Peter, Van de Vondel, Liedewei, De Ridder, Willem, Weckhuysen, Sarah, Nigro, Vincenzo, Mutarelli, Margherita, Varavallo, Alessandra, Banfi, Sandro, Musacchia, Francesco, Piluso, Giulio, Ferlini, Alessandra, Selvatici, Rita, Gualandi, Francesca, Bigoni, Stefania, 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 Vries, Gerben, Neerincx, Pieter B., Ruvolo, David, Kerstjens Frederikse, Wilhemina S., Zonneveld-Huijssoon, Eveline, Roelofs-Prins, Dieuwke, van Gijn, Marielle, Köhler, Sebastian, Metcalfe, Alison, Drunat, Séverine, Heron, Delphine, Mignot, Cyril, Keren, Boris, Lacombe, Didier, Trimouille, Aurelien, Capella, Gabriel, Valle, Laura, Holinski-Feder, Elke, Laner, Andreas, Steinke-Lange, Verena, Cilio, Maria-Roberta, Carpancea, Evelina, Depondt, Chantal, Lederer, Damien, Sznajer, Yves, Duerinckx, Sarah, Mary, Sandrine, Macaya, Alfons, Cazurro-Gutiérrez, Ana, Pérez-Dueñas, Belén, Munell, Francina, Jarava, Clara Franco, Masó, Laura Batlle, Marcé-Grau, Anna, Colobran, Roger, Hackman, Peter, Udd, Bjarne, Hemelsoet, Dimitri, Dermaut, Bart, Schuermans, Nika, Poppe, Bruce, Verdin, Hannah, Osorio, Andrés Nascimento, Depienne, Christel, Roos, Andreas, Cordts, Isabell, Deschauer, Marcus, Striano, Pasquale, Zara, Federico, Riva, Antonella, Iacomino, Michele, Uva, Paolo, Scala, Marcello, Scudieri, Paolo, Claeys, Kristl, Boztug, Kaan, Haimel, Matthias, W.E, Gijs, Ruivenkamp, Claudia A. L., Natera de Benito, Daniel, Thompson, Rachel, Polavarapu, Kiran, Grimbacher, Bodo, Zaganas, Ioannis, Kokosali, Evgenia, Lambros, Mathioudakis, Evangeliou, Athanasios, Spilioti, Martha, Kapaki, Elisabeth, Bourbouli, Mara, Balicza, Peter, Molnar, Maria Judit, De la Paz, Manuel Posada, Sánchez, Eva Bermejo, Delgado, Beatriz Martínez, Alonso García de la Rosa, F. Javier, Schröck, Evelin, Rump, Andreas, Mei, Davide, Vetro, Annalisa, Balestrini, Simona, Guerrini, Renzo, Chinnery, Patrick F., Ratnaike, Thiloka, Schon, Katherine, Maver, Ales, Peterlin, Borut, Münchau, Alexander, Lohmann, Katja, Herzog, Rebecca, Pauly, Martje, May, Patrick, Beeson, David, Cossins, Judith, Furini, Simone, Afenjar, Alexandra, Goldenberg, Alice, Masurel, Alice, Phan, Alice, Dieux-Coeslier, Anne, Fargeot, Anne, Guerrot, Anne-Marie, Toutain, Annick, Molin, Arnaud, Sorlin, Arthur, Putoux, Audrey, Jouret, Béatrice, Laudier, Béatrice, Demeer, Bénédicte, Doray, Bérénice, Bonniaud, Bertille, Isidor, Bertrand, Gilbert-Dussardier, Brigitte, Leheup, Bruno, Reversade, Bruno, Paul, Carle, Vincent-Delorme, Catherine, Neiva, Cecilia, Poirsier, Céline, Quélin, Chloé, Chiaverini, Christine, Coubes, Christine, Francannet, Christine, Colson, Cindy, Desplantes, Claire, Wells, Constance, Goizet, Cyril, Sanlaville, Damien, Amram, Daniel, Lehalle, Daphné, Geneviève, David, Gaillard, Dominique, Zivi, Einat, Sarrazin, Elisabeth, Steichen, Elisabeth, Schaefer, Élise, Lacaze, Elodie, Jacquemin, Emmanuel, Bongers, Ernie, Kilic, Esra, Colin, Estelle, Giuliano, Fabienne, Prieur, Fabienne, Laffargue, Fanny, Morice-Picard, Fanny, Petit, Florence, Cartault, François, Feillet, François, Baujat, Geneviève, Morin, Gilles, Diene, Gwenaëlle, Journel, Hubert, Perthus, Isabelle, Lespinasse, James, Alessandri, Jean-Luc, Amiel, Jeanne, Martinovic, Jelena, Delanne, Julian, Albuisson, Juliette, Lambert, Laëtitia, Perrin, Laurence, Ousager, Lilian Bomme, Van Maldergem, Lionel, Pinson, Lucile, Ruaud, Lyse, Samimi, Mahtab, Bournez, Marie, Bonnet-Dupeyron, Marie Noëlle, Vincent, Marie, Jacquemont, Marie-Line, Cordier-Alex, Marie-Pierre, Gérard-Blanluet, Marion, Willems, Marjolaine, Spodenkiewicz, Marta, Doco-Fenzy, Martine, Rossi, Massimiliano, Renaud, Mathilde, Fradin, Mélanie, Mathieu, Michèle, Holder-Espinasse, Muriel H., Houcinat, Nada, Hanna, Nadine, Leperrier, Nathalie, Chassaing, Nicolas, Philip, Nicole, Boute, Odile, Van Kien, Philippe Khau, Parent, Philippe, Bitoun, Pierre, Sarda, Pierre, Vabres, Pierre, Jouk, Pierre-Simon, Touraine, Renaud, El Chehadeh, Salima, Whalen, Sandra, Marlin, Sandrine, Passemard, Sandrine, Grotto, Sarah, Bellanger, Séverine Audebert, Blesson, Sophie, Nambot, Sophie, Naudion, Sophie, Lyonnet, Stanislas, Odent, Sylvie, Attie-Bitach, Tania, Busa, Tiffany, Drouin-Garraud, Valérie, Layet, Valérie, Bizaoui, Varoona, Cusin, Véronica, Capri, Yline, and Alembik, Yves

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.

Published
2023

4. Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples

Author

Wijngaard, Robin, Demidov, German, O’Gorman, Luke, Corominas-Galbany, Jordi, Yaldiz, Burcu, Steyaert, Wouter, de Boer, Elke, Vissers, Lisenka E. L. M., Kamsteeg, Erik-Jan, Pfundt, Rolph, Swinkels, Hilde, den Ouden, Amber, te Paske, Iris B. A. W., de Voer, Richarda M., Faivre, Laurence, Denommé-Pichon, Anne-Sophie, Duffourd, Yannis, Vitobello, Antonio, Chevarin, Martin, Straub, Volker, Töpf, Ana, van der Kooi, Anneke J., Magrinelli, Francesca, Rocca, Clarissa, Hanna, Michael G., Vandrovcova, Jana, Ossowski, Stephan, Laurie, Steven, and Gilissen, Christian

Abstract

Mobile element insertions (MEIs) are a known cause of genetic disease but have been underexplored due to technical limitations of genetic testing methods. Various bioinformatic tools have been developed to identify MEIs in Next Generation Sequencing data. However, most tools have been developed specifically for genome sequencing (GS) data rather than exome sequencing (ES) data, which remains more widely used for routine diagnostic testing. In this study, we benchmarked six MEI detection tools (ERVcaller, MELT, Mobster, SCRAMble, TEMP2 and xTea) on ES data and on GS data from publicly available genomic samples (HG002, NA12878). For all the tools we evaluated sensitivity and precision of different filtering strategies. Results show that there were substantial differences in tool performance between ES and GS data. MELT performed best with ES data and its combination with SCRAMble increased substantially the detection rate of MEIs. By applying both tools to 10,890 ES samples from Solve-RD and 52,624 samples from Radboudumc we were able to diagnose 10 patients who had remained undiagnosed by conventional ES analysis until now. Our study shows that MELT and SCRAMble can be used reliably to identify clinically relevant MEIs in ES data. This may lead to an additional diagnosis for 1 in 3000 to 4000 patients in routine clinical ES.

Published
2024
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5. Germline mutations inWNK2could be associated with serrated polyposis syndrome

Author

Soares de Lima, Yasmin, primary, Arnau-Collell, Coral, additional, Muñoz, Jenifer, additional, Herrera-Pariente, Cristina, additional, Moreira, Leticia, additional, Ocaña, Teresa, additional, Díaz-Gay, Marcos, additional, Franch-Expósito, Sebastià, additional, Cuatrecasas, Miriam, additional, Carballal, Sabela, additional, Lopez-Novo, Anael, additional, Moreno, Lorena, additional, Fernàndez, Guerau, additional, Díaz de Bustamante, Aranzazu, additional, Peters, Sophia, additional, Sommer, Anna K, additional, Spier, Isabel, additional, te Paske, Iris B A W, additional, van Herwaarden, Yasmijn J, additional, Castells, Antoni, additional, Bujanda, Luis, additional, Capellà, Gabriel, additional, Steinke-Lange, Verena, additional, Mahmood, Khalid, additional, Joo, JiHoon Eric, additional, Arnold, Julie, additional, Parry, Susan, additional, Macrae, Finlay A, additional, Winship, Ingrid M, additional, Rosty, Christophe, additional, Cubiella, Joaquin, additional, Rodríguez-Alcalde, Daniel, additional, Holinski-Feder, Elke, additional, de Voer, Richarda, additional, Buchanan, Daniel D, additional, Aretz, Stefan, additional, Ruiz-Ponte, Clara, additional, Valle, Laura, additional, Balaguer, Francesc, additional, Bonjoch, Laia, additional, and Castellvi-Bel, Sergi, additional

Published
2022
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6. Germline mutations in WNK2 could be associated with serrated polyposis syndrome.

Author

de Lima, Yasmin Soares, Arnau-Collell, Coral, Muñoz, Jenifer, Herrera-Pariente, Cristina, Moreira, Leticia, Ocaña, Teresa, Díaz-Gay, Marcos, Franch-Expósito, Sebastià, Cuatrecasas, Miriam, Carballal, Sabela, Lopez-Novo, Anael, Moreno, Lorena, Fernàndez, Guerau, Díaz de Bustamante, Aranzazu, Peters, Sophia, Sommer, Anna K., Spier, Isabel, te Paske, Iris B. A. W., van Herwaarden, Yasmijn J., and Castells, Antoni

Abstract

Background: Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts. Methods: After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion. Results: We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2. Conclusion: After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease. [ABSTRACT FROM AUTHOR]

Published
2023
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7. Germline mutations in WNK2could be associated with serrated polyposis syndrome

Author

Soares de Lima, Yasmin, Arnau-Collell, Coral, Muñoz, Jenifer, Herrera-Pariente, Cristina, Moreira, Leticia, Ocaña, Teresa, Díaz-Gay, Marcos, Franch-Expósito, Sebastià, Cuatrecasas, Miriam, Carballal, Sabela, Lopez-Novo, Anael, Moreno, Lorena, Fernàndez, Guerau, Díaz de Bustamante, Aranzazu, Peters, Sophia, Sommer, Anna K, Spier, Isabel, te Paske, Iris B A W, van Herwaarden, Yasmijn J, Castells, Antoni, Bujanda, Luis, Capellà, Gabriel, Steinke-Lange, Verena, Mahmood, Khalid, Joo, JiHoon Eric, Arnold, Julie, Parry, Susan, Macrae, Finlay A, Winship, Ingrid M, Rosty, Christophe, Cubiella, Joaquin, Rodríguez-Alcalde, Daniel, Holinski-Feder, Elke, de Voer, Richarda, Buchanan, Daniel D, Aretz, Stefan, Ruiz-Ponte, Clara, Valle, Laura, Balaguer, Francesc, Bonjoch, Laia, and Castellvi-Bel, Sergi

Abstract

BackgroundPatients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts.MethodsAfter a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2gene was disrupted in HT-29 cells by gene editing, and WNK2variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion.ResultsWe identified 2 rare germline variants in the WNK2gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2.ConclusionAfter whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2gene. Functional studies suggested germline WNK2variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease.

Published
2023
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8. Detection and characterization of mosaicism in autosomal dominant polycystic kidney disease

Author

Hopp, Katharina, Cornec-Le Gall, Emilie, Senum, Sarah R., te Paske, Iris B. A. W., Raj, Sonam, Lavu, Sravanthi, Baheti, Saurabh, Edwards, Marie E., Madsen, Charles D., Heyer, Christina M., Ong, Albert C. M., Bae, Kyongtae T., Fatica, Richard, Steinman, Theodore, Chapman, Arlene B., Gitomer, Berenice, Perrone, Ronald D., Rahbari-Oskoui, Frederic F., Torres, Vicente E., Braun, W. E., Czarnecki, P. G., Chebib, F. T., Hogan, M. C., Mrug, M., Pei, Y., Sandford, R., Mayo Clinic [Rochester], Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), University of Sheffield [Sheffield], University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), Cleveland Clinic, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS), Emory University School of Medicine, Emory University [Atlanta, GA], University of Colorado [Denver], Tufts University School of Medicine [Boston], PODEUR, Sophie, Cardiovascular Centre (CVC), and Groningen Kidney Center (GKC)

Subjects
0301 basic medicine, TRPP Cation Channels, [SDV]Life Sciences [q-bio], Population, PKD1, 030232 urology & nephrology, Autosomal dominant polycystic kidney disease, PROGRESSION, Biology, DIAGNOSIS, urologic and male genital diseases, Nephropathy, End stage renal disease, 03 medical and health sciences, 0302 clinical medicine, prognostics, Genotype, medicine, diagnostics, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Humans, Family history, education, ADPKD, Genetics, education.field_of_study, IDENTIFICATION, urogenital system, High-Throughput Nucleotide Sequencing, medicine.disease, Polycystic Kidney, Autosomal Dominant, genotype/phenotype correlations, mutations, GENE, female genital diseases and pregnancy complications, GENOTYPE, [SDV] Life Sciences [q-bio], 030104 developmental biology, mosaicism, Nephrology, Mutation, Female, Kidney disease
Abstract

International audience; Autosomal dominant polycystic kidney disease (ADPKD) is an inherited, progressive nephropathy accounting for 4-10% of end stage renal disease worldwide. PKD1 and PKD2 are the most common disease loci, but even accounting for other genetic causes, about 7% of families remain unresolved. Typically, these unsolved cases have relatively mild kidney disease and often have a negative family history. Mosaicism, due to de novo mutation in the early embryo, has rarely been identified by conventional genetic analysis of ADPKD families. Here we screened for mosaicism by employing two next generation sequencing screens, specific analysis of PKD1 and PKD2 employing long-range polymerase chain reaction, or targeted capture of cystogenes. We characterized mosaicism in 20 ADPKD families; the pathogenic variant was transmitted to the next generation in five families and sporadic in 15. The mosaic pathogenic variant was newly discovered by next generation sequencing in 13 families, and these methods precisely quantified the level of mosaicism in all. All of the mosaic cases had PKD1 mutations, 14 were deletions or insertions, and 16 occurred in females. Analysis of kidney size and function showed the mosaic cases had milder disease than a control PKD1 population, but only a few had clearly asymmetric disease. Thus, in a typical ADPKD population, readily detectable mosaicism by next generation sequencing accounts for about 1% of cases, and about 10% of genetically unresolved cases with an uncertain family history. Hence, identification of mosaicism is important to fully characterize ADPKD populations and provides informed prognostic information.

Published
2020
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10. A mosaic PIK3CAvariant in a young adult with diffuse gastric cancer: case report

Author

te Paske, Iris B. A. W., Garcia-Pelaez, José, Sommer, Anna K., Matalonga, Leslie, Starzynska, Teresa, Jakubowska, Anna, van der Post, Rachel S., Lubinski, Jan, Oliveira, Carla, Hoogerbrugge, Nicoline, and de Voer, Richarda M.

Abstract

Hereditary diffuse gastric cancer (HDGC) is associated with germline deleterious variants in CDH1and CTNNA1. The majority of HDGC-suspected patients are still genetically unresolved, raising the need for identification of novel HDGC predisposing genes. Under the collaborative environment of the SOLVE-RD consortium, re-analysis of whole-exome sequencing data from unresolved gastric cancer cases (n= 83) identified a mosaic missense variant in PIK3CAin a 25-year-old female with diffuse gastric cancer (DGC) without familial history for cancer. The variant, c.3140A>G p.(His1047Arg), a known cancer-related somatic hotspot, was present at a low variant allele frequency (18%) in leukocyte-derived DNA. Somatic variants in PIK3CAare usually associated with overgrowth, a phenotype that was not observed in this patient. This report highlights mosaicism as a potential, and understudied, mechanism in the etiology of DGC.

Published
2021
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12. Germline mutations in WNK2 could be associated with serrated polyposis syndrome.

Author

Soares de Lima Y, Arnau-Collell C, Muñoz J, Herrera-Pariente C, Moreira L, Ocaña T, Díaz-Gay M, Franch-Expósito S, Cuatrecasas M, Carballal S, Lopez-Novo A, Moreno L, Fernàndez G, Díaz de Bustamante A, Peters S, Sommer AK, Spier I, Te Paske IBAW, van Herwaarden YJ, Castells A, Bujanda L, Capellà G, Steinke-Lange V, Mahmood K, Joo JE, Arnold J, Parry S, Macrae FA, Winship IM, Rosty C, Cubiella J, Rodríguez-Alcalde D, Holinski-Feder E, de Voer R, Buchanan DD, Aretz S, Ruiz-Ponte C, Valle L, Balaguer F, Bonjoch L, and Castellvi-Bel S

Subjects
Humans, Germ-Line Mutation genetics, Genotype, Protein Serine-Threonine Kinases genetics, Adenomatous Polyposis Coli genetics, Colonic Polyps genetics, Colorectal Neoplasms genetics
Abstract

Background: Patients with serrated polyposis syndrome (SPS) have multiple and/or large serrated colonic polyps and higher risk for colorectal cancer. SPS inherited genetic basis is mostly unknown. We aimed to identify new germline predisposition factors for SPS by functionally evaluating a candidate gene and replicating it in additional SPS cohorts., Methods: After a previous whole-exome sequencing in 39 SPS patients from 16 families (discovery cohort), we sequenced specific genes in an independent validation cohort of 211 unrelated SPS cases. Additional external replication was also available in 297 SPS cases. The WNK2 gene was disrupted in HT-29 cells by gene editing, and WNK2 variants were transfected using a lentiviral delivery system. Cells were analysed by immunoblots, real-time PCR and functional assays monitoring the mitogen-activated protein kinase (MAPK) pathway, cell cycle progression, survival and adhesion., Results: We identified 2 rare germline variants in the WNK2 gene in the discovery cohort, 3 additional variants in the validation cohort and 10 other variants in the external cohorts. Variants c.2105C>T (p.Pro702Leu), c.4820C>T (p.Ala1607Val) and c.6157G>A (p.Val2053Ile) were functionally characterised, displaying higher levels of phospho-PAK1/2, phospho-ERK1/2, CCND1, clonogenic capacity and MMP2., Conclusion: After whole-exome sequencing in SPS cases with familial aggregation and replication of results in additional cohorts, we identified rare germline variants in the WNK2 gene. Functional studies suggested germline WNK2 variants affect protein function in the context of the MAPK pathway, a molecular hallmark in this disease., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

Published
2023
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13. Wnt genes in colonic polyposis predisposition.

Author

Quintana I, Terradas M, Mur P, Te Paske IBAW, Peters S, Spier I, Steinke-Lange V, Maestro C, Torrents D, Puiggròs M, Royo R, Tonda R, Parra G, Piscia D, Beltrán S, Navarro M, Piñol V, Brunet J, Gonzalez-Abuin N, Aiza G, Sommer A, van Herwaarden Y, Astuti G, Holinski-Feder E, Hoogerbrugge N, de Voer RM, Aretz S, Capellá G, and Valle L

Published
2022
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15. Solving the genetic aetiology of hereditary gastrointestinal tumour syndromes- a collaborative multicentre endeavour within the project Solve-RD.

Author

Sommer AK, Te Paske IBAW, Garcia-Pelaez J, Laner A, Holinski-Feder E, Steinke-Lange V, Peters S, Valle L, Spier I, Huntsman D, Oliveira C, de Voer RM, Hoogerbrugge N, and Aretz S

Subjects
Genetic Predisposition to Disease, Genomics, Humans, Exome Sequencing, Colorectal Neoplasms genetics, Neoplastic Syndromes, Hereditary genetics
Abstract

Background: Patients and families with suspected, but genetically unexplained (unsolved) genetic tumour risk syndromes lack appropriate treatment and prevention, leading to preventable morbidity and mortality. To tackle this problem, patients from the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) are analysed in the European Commission's research project "Solving the unsolved rare diseases" (Solve-RD). The aim is to uncover known and novel cancer predisposing genes by reanalysing available whole-exome sequencing (WES) data of large cohorts in a combined manner, and applying a multidimensional omics approach., Approach: Around 500 genetically unsolved cases with suspected hereditary gastrointestinal tumour syndromes (polyposis, early-onset/familial colorectal cancer and gastric cancer) from multiple European centres are aimed to be included. Currently, clinical and germline WES data from 294 cases have been analysed. In addition, an extensive molecular profiling of gastrointestinal tumours from these patients is planned and deep learning techniques will be applied. The ambitious, multidisciplinary project is accompanied by a number of methodical, technical, and logistic challenges, which require the development and implementation of new analysis tools, the standardisation of bioinformatics pipelines, and strategies to exchange data and knowledge., Results: and Outlook. The first re-analysis of 229 known and proposed cancer predisposition genes allowed solving 2-3% of previously unsolved GENTURIS cases. The integration of expert knowledge and new technologies will help to identify the genetic basis of additional unsolved cases within the ongoing project. The ERN GENTURIS approach might serve as a model for other genomic initiatives., (Copyright © 2022. Published by Elsevier Masson SAS.)

Published
2022
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16. A mosaic PIK3CA variant in a young adult with diffuse gastric cancer: case report.

Author

Te Paske IBAW, Garcia-Pelaez J, Sommer AK, Matalonga L, Starzynska T, Jakubowska A, van der Post RS, Lubinski J, Oliveira C, Hoogerbrugge N, and de Voer RM

Subjects
Adult, Female, Humans, Mutation, Missense, Stomach Neoplasms pathology, Exome Sequencing, Class I Phosphatidylinositol 3-Kinases genetics, Mosaicism, Stomach Neoplasms genetics
Abstract

Hereditary diffuse gastric cancer (HDGC) is associated with germline deleterious variants in CDH1 and CTNNA1. The majority of HDGC-suspected patients are still genetically unresolved, raising the need for identification of novel HDGC predisposing genes. Under the collaborative environment of the SOLVE-RD consortium, re-analysis of whole-exome sequencing data from unresolved gastric cancer cases (n = 83) identified a mosaic missense variant in PIK3CA in a 25-year-old female with diffuse gastric cancer (DGC) without familial history for cancer. The variant, c.3140A>G p.(His1047Arg), a known cancer-related somatic hotspot, was present at a low variant allele frequency (18%) in leukocyte-derived DNA. Somatic variants in PIK3CA are usually associated with overgrowth, a phenotype that was not observed in this patient. This report highlights mosaicism as a potential, and understudied, mechanism in the etiology of DGC., (© 2021. The Author(s).)

Published
2021
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17. Detection and characterization of mosaicism in autosomal dominant polycystic kidney disease.

Author

Hopp K, Cornec-Le Gall E, Senum SR, Te Paske IBAW, Raj S, Lavu S, Baheti S, Edwards ME, Madsen CD, Heyer CM, Ong ACM, Bae KT, Fatica R, Steinman TI, Chapman AB, Gitomer B, Perrone RD, Rahbari-Oskoui FF, Torres VE, and Harris PC

Subjects
Female, High-Throughput Nucleotide Sequencing, Humans, Mosaicism, Mutation, TRPP Cation Channels genetics, Polycystic Kidney, Autosomal Dominant diagnosis, Polycystic Kidney, Autosomal Dominant genetics
Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited, progressive nephropathy accounting for 4-10% of end stage renal disease worldwide. PKD1 and PKD2 are the most common disease loci, but even accounting for other genetic causes, about 7% of families remain unresolved. Typically, these unsolved cases have relatively mild kidney disease and often have a negative family history. Mosaicism, due to de novo mutation in the early embryo, has rarely been identified by conventional genetic analysis of ADPKD families. Here we screened for mosaicism by employing two next generation sequencing screens, specific analysis of PKD1 and PKD2 employing long-range polymerase chain reaction, or targeted capture of cystogenes. We characterized mosaicism in 20 ADPKD families; the pathogenic variant was transmitted to the next generation in five families and sporadic in 15. The mosaic pathogenic variant was newly discovered by next generation sequencing in 13 families, and these methods precisely quantified the level of mosaicism in all. All of the mosaic cases had PKD1 mutations, 14 were deletions or insertions, and 16 occurred in females. Analysis of kidney size and function showed the mosaic cases had milder disease than a control PKD1 population, but only a few had clearly asymmetric disease. Thus, in a typical ADPKD population, readily detectable mosaicism by next generation sequencing accounts for about 1% of cases, and about 10% of genetically unresolved cases with an uncertain family history. Hence, identification of mosaicism is important to fully characterize ADPKD populations and provides informed prognostic information., (Copyright © 2019 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

Published
2020
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