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Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

Title: Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses
Authors: Demidov, German; Yaldiz, Burcu; Garcia-Pelaez, José; de Boer, Elke; Schuermans, Nika; Van de Vondel, Liedewei; Paramonov, Ida; Johansson, Lennart F.; Musacchia, Francesco; Benetti, Elisa; Bullich, Gemma; Sablauskas, Karolis; Beltran, Sergi; Gilissen, Christian; Hoischen, Alexander; Ossowski, Stephan; de Voer, Richarda; Lohmann, Katja; Oliveira, Carla; Topf, Ana; Vissers, Lisenka E. L. M.; null, null; Riess, Olaf; Haack, Tobias B.; Graessner, Holm; Zurek, Birte; Ellwanger, Kornelia; Sturm, Marc; Park, Joohyun; Schütz, Leon; Schulze-Hentrich, Julia M.; Schüle, Rebecca; Xu, Jishu; Kellner, Melanie; Resch, Baptist; Kolen, Ingrid; Synofzik, Matthis; Wilke, Carlo; Traschütz, Andreas; Beijer, Danique; Heutink, Peter; Schöls, Ludger; Hengel, Holger; Lerche, Holger; Boßelmann, Christian; Kegele, Josua; Lauerer-Braun, Robert; Lauxmann, Stephan; Brunner, Han; Scheffer, Hans; Hoogerbrugge, Nicoline; 't Hoen, Peter A. C.; Steyaert, Wouter; Kamsteeg, Erik-Jan; van de Warrenburg, Bart; van Os, Nienke; Paske, Iris te; Janssen, Erik; Steehouwer, Marloes; Neveling, Kornelia; van der Sanden, Bart; Sagath, Lydia; Kleefstra, Tjitske; Brookes, Anthony J.; Gibson, Spencer; Riaz, Umar; Warren, Greg; Nalagandla, Sai Anuhya; Wang, Yunze Patrick; Sukumaran, Deepthi; Abadijou, Sadegh; Straub, Volker; Bettolo, Chiara Marini; Manera, Jordi Diaz; Hambleton, Sophie; Engelhardt, Karin; Clayton-Smith, Jill; Banka, Siddharth; Alexander, Elizabeth; Jackson, Adam; Faivre, Laurence; Thauvin, Christel; Vitobello, Antonio; Denommé-Pichon, Anne-Sophie; Duffourd, Yannis; Bruel, Ange-Line; Couturier, Victor; Gut, Ivo Glynne; Piscia, Davide; Matalonga, Leslie; Papakonstantinou, Anastasios; Corvo, Alberto; Fernandez-Callejo, Marcos; Hernández, Carles; Picó, Daniel; Codina, Anna Esteve; Dabad, Marc; Gut, Marta; Raineri, Emanuele; Gumus, Gulcin; Bros-Facer, Virginie; Rath, Ana; Hanauer, Marc; Lagorce, David; Hongnat, Oscar; Chahdil, Maroua; Lucano, Caterina; Lebreton, Emeline; Stevanin, Giovanni; Durr, Alexandra; Davoine, Claire-Sophie; Guillot-Noel, Léna; Heinzmann, Anna; Coarelli, Giulia; Bonne, Gisèle; Evangelista, Teresinha; Allamand, Valérie; Nelson, Isabelle; Ben Yaou, Rabah; Metay, Corinne; Eymard, Bruno; Cohen, Enzo; Atalaia, Antonio; Stojkovic, Tanya; Macek, Milan; Turnovec, Marek; Thomasová, Dana; Kremliková, Radka Pourová; Franková, Vera; Havlovicová, Markéta; Ryba, Lukáš; Lišková, Petra; Doležalová, Pavla; Krebsová, Alice; Parkinson, Helen; Keane, Thomas; Freeberg, Mallory; Thomas, Coline; Spalding, Dylan; Robinson, Peter; Danis, Daniel; Robert, Glenn; Costa, Alessia; Hanna, Mike; Houlden, Henry; Reilly, Mary; Vandrovcova, Jana; Efthymiou, Stephanie; Morsy, Heba; Cali, Elisa; Magrinelli, Francesca; Sisodiya, Sanjay M.; Bellampalli, Ravishankara; Moloney, Patrick; Rohrer, Jonathan; Muntoni, Francesco; Zaharieva, Irina; Sarkozy, Anna; Perry, Luke; Pini, Veronica; Müller, Juliane; Timmerman, Vincent; Baets, Jonathan; de Vries, Geert; De Winter, Jonathan; de Jonghe, Peter; De Ridder, Willem; Weckhuysen, Sarah; Stamberger, Hannah; Millevert, Charissa; Smal, Noor; Nigro, Vincenzo; Morleo, Manuela; Pinelli, Michele; Banfi, Sandro; Torella, Annalaura; Zeuli, Roberta; Zanobio, Mariateresa; Piluso, Giulio; Ferlini, Alessandra; Selvatici, Rita; Gualandi, Francesca; Bigoni, Stefania; Neri, Marcella; Aretz, Stefan; Spier, Isabel; Sommer, Anna Katharina; Peters, Sophia; Barbosa-Matos, Rita; José, Celina São; Ferreira, Marta; Gullo, Irene; Fernandes, Susana; Garrido, Luzia; Ferreira, Pedro; Carneiro, Fátima; Swertz, Morris A.; van der Velde, Joeri K.; van der Vries, Gerben; Neerincx, Pieter B.; Roelofs-Prins, Dieuwke; Ruvolo, David; van Gijn, Marielle; Abbott, Kristin M.; Kerstjens Frederikse, Wilhemina S.; Zonneveld-Huijssoon, Eveline; Köhler, Sebastian; Metcalfe, Alison; Moore, Richard; Verloes, Alain; Drunat, Séverine; Heron, Delphine; Mignot, Cyril; Keren, Boris; de Sainte Agathe, Jean-Madeleine; Jamra, Rami Abou; Abramowicz, Marc; Kiliçarslan, Özge Aksel; Allen, Nicholas; Javier Alonso García de la Rosa, Francisco; Balestrini, Simona; Balicza, Peter; Bartolomaeus, Tobias; Başak, Ayşe Nazl; Masó, Laura Batlle; Beeson, David; Benoit, Valerie; Benson, Katherine; Sánchez, Eva Bermejo; Bijlsma, Emilia K.; Bogaert, Elke; Bourbouli, Mara; Boztug, Kaan; Brohée, Sylvain; Byrne, Susan; Garcia de Oteyza, Andrés Caballero; Capella, Gabriel; Carpancea, Evelina; Cavalleri, Gianpiero; Cazurro-Gutiérrez, Ana; Chinnery, Patrick F.; Cilio, Maria-Roberta; Ciolfi, Andrea; Claeys, Kristl; Colobran, Roger; Cordts, Isabell; Cossins, Judith; Dahan, Karin; Dallapiccola, Bruno; Delanty, Norman; Depienne, Christel; Depondt, Chantal; Dermaut, Bart; Deschauer, Marcus; Desir, Julie; Destrée, Anne; Drakos, Minas; Duerinckx, Sarah; Estevez, Berta; Evangeliou, Athanasios; Fallerini, Chiara; Ferilli, Marco; Furini, Simone; Gagneur, Julien; Ghani, Hamidah; Greally, Marie; Grimbacher, Bodo; Guerrini, Renzo; Hackman, Peter; Haimel, Matthias; Bouveret, Eva Hammar; Hemelsoet, Dimitri; Herzog, Rebecca; Hoffer, Mariette J. V.; Holinski-Feder, Elke; Horvath, Rita; Huibers, Manon; Iacomino, Michele; Johari, Mridul; Kapaki, Elisabeth; Karadurmus, Deniz; Karakaya, Mert; Kokosali, Evgenia; Korff, Christian; Krass, Leon; Lacombe, Didier; Laner, Andreas; Leavis, Helen; Lederer, Damien; Leitão, Elsa; Lochmüller, Hanns; Martín, Estrella López; Luknárová, Rebeka; Macaya, Alfons; Malaichamy, Sivasankar; Marcé-Grau, Anna; Delgado, Beatriz Martínez; Mary, Sandrine; Masclaux, Frédéric; Mathioudakis, Lambros; Maver, Ales; May, Patrick; Maystadt, Isabelle; Mei, Davide; Mertes, Christian; Meunier, Colombine; Molnar, Maria Judit; Monestier, Olivier; Moortgat, Stéphanie; Münchau, Alexander; Munell, Francina; Osorio, Andrés Nascimento; de Benito, Daniel Natera; Reghan, Mary O.; Olimpio, Catarina; Parrini, Elena; Pauly, Martje; Pérez-Dueñas, Belén; Peterlin, Borut; Platzer, Konrad; Polavarapu, Kiran; Poppe, Bruce; De la Paz, Manuel Posada; Privitera, Flavia; Radio, Francesca Clementina; Ratnaike, Thiloka; Renieri, Alessandra; Riva, Antonella; Rooryck, Caroline; Roos, Andreas; Ruivenkamp, Claudia A. L.; Rump, Andreas; Santen, Gijs W. E.; Savarese, Marco; Scala, Marcello; Schon, Katherine; Schröck, Evelin; Scudieri, Paolo; Spilioti, Martha; Steinke-Lange, Verena; Striano, Pasquale; Sznajer, Yves; Tartaglia, Marco; Thompson, Rachel; Trimouille, Aurelien; Udd, Bjarne; Uva, Paolo; Valle, Laura; van der Veken, Lars; van Heurck, Roxane; van Montfrans, Joris; Van Nieuwenhove, Erika; Verdin, Hannah; Webb, David; Wirth, Brunhilde; Yépez, Vicente A.; Zaganas, Ioannis; Zara, Federico; Zguro, Kristina; Laurie, Steven
Contributors: Demidov, German; Yaldiz, Burcu; Garcia-Pelaez, José; de Boer, Elke; Schuermans, Nika; Van de Vondel, Liedewei; Paramonov, Ida; Johansson, Lennart F.; Musacchia, Francesco; Benetti, Elisa; Bullich, Gemma; Sablauskas, Karoli; Beltran, Sergi; Gilissen, Christian; Hoischen, Alexander; Ossowski, Stephan; de Voer, Richarda; Lohmann, Katja; Oliveira, Carla; Topf, Ana; Vissers, Lisenka E. L. M.; Null, Null; Riess, Olaf; Haack, Tobias B.; Graessner, Holm; Zurek, Birte; Ellwanger, Kornelia; Sturm, Marc; Park, Joohyun; Schütz, Leon; Schulze-Hentrich, Julia M.; Schüle, Rebecca; Xu, Jishu; Kellner, Melanie; Resch, Baptist; Kolen, Ingrid; Synofzik, Matthi; Wilke, Carlo; Traschütz, Andrea; Beijer, Danique; Heutink, Peter; Schöls, Ludger; Hengel, Holger; Lerche, Holger; Boßelmann, Christian; Kegele, Josua; Lauerer-Braun, Robert; Lauxmann, Stephan; Brunner, Han; Scheffer, Han; Hoogerbrugge, Nicoline; 't Hoen, Peter A. C.; Steyaert, Wouter; Kamsteeg, Erik-Jan; van de Warrenburg, Bart; van Os, Nienke; Paske, Iris te; Janssen, Erik; Steehouwer, Marloe; Neveling, Kornelia; van der Sanden, Bart; Sagath, Lydia; Kleefstra, Tjitske; Brookes, Anthony J.; Gibson, Spencer; Riaz, Umar; Warren, Greg; Nalagandla, Sai Anuhya; Wang, Yunze Patrick; Sukumaran, Deepthi; Abadijou, Sadegh; Straub, Volker; Bettolo, Chiara Marini; Manera, Jordi Diaz; Hambleton, Sophie; Engelhardt, Karin; Clayton-Smith, Jill; Banka, Siddharth; Alexander, Elizabeth; Jackson, Adam; Faivre, Laurence; Thauvin, Christel; Vitobello, Antonio; Denommé-Pichon, Anne-Sophie; Duffourd, Yanni; Bruel, Ange-Line; Couturier, Victor; Gut, Ivo Glynne; Piscia, Davide; Matalonga, Leslie; Papakonstantinou, Anastasio; Corvo, Alberto; Fernandez-Callejo, Marco; Hernández, Carle; Picó, Daniel; Codina, Anna Esteve; Dabad, Marc; Gut, Marta
Publication Year: 2024
Collection: Università degli Studi di Siena: USiena air
Description: We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs.
Document Type: article in journal/newspaper
File Description: ELETTRONICO
Language: English
Relation: info:eu-repo/semantics/altIdentifier/pmid/39461972; info:eu-repo/semantics/altIdentifier/wos/WOS:001681426400001; volume:9; issue:1; numberofpages:24; journal:NPJ GENOMIC MEDICINE; https://hdl.handle.net/11365/1277026; https://pmc.ncbi.nlm.nih.gov/articles/PMC11513043/
DOI: 10.1038/s41525-024-00436-6
Availability: https://hdl.handle.net/11365/1277026; https://doi.org/10.1038/s41525-024-00436-6; https://www.nature.com/articles/s41525-024-00436-6; https://pmc.ncbi.nlm.nih.gov/articles/PMC11513043/
Rights: info:eu-repo/semantics/openAccess ; license:Creative commons ; license uri:http://creativecommons.org/licenses/by/4.0/
Accession Number: edsbas.2F72730C
Database: BASE