Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

作者：Burcu Yaldız, Erdi Küçük, Juliet E. Hampstead, Tom Hofste, Rolph Pfundt, Jordi Corominas Galbany, Tuula Rinne, Helger G. Yntema, Alexander Hoischen, Marcel Nelen, Christian Gilissen, Olaf Rieß, Tobias B. Haack, Holm Graeßner, Birte Zurek, Kornelia Ellwanger, Stephan Ossowski, German Demidov, Marc Sturm, Julia M. Schulze‐Hentrich, Rebecca Schüle, Jishu Xu, Christoph Keßler, Melanie Wayand, Matthis Synofzik, Carlo Wilke, Andreas Traschütz, Lüdger Schöls, Holger Hengel, Holger Lerche, Josua Kegele, Peter Heutink, Han G. Brunner, Hans Scheffer, Nicoline Hoogerbrugge, Alexander Hoischen, Peter A.C. ’t Hoen, Lisenka E.L.M. Vissers, Christian Gilissen, Wouter Steyaert, Karolis Šablauskas, 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 Yaldız, Tjitske Kleefstra, Anthony J. Brookes, Colin Veal, Spencer Gibson, Vatsalya Maddi, Mehdi Mehtarizadeh, Umar Riaz, Greg Warren, Farid Yavari Dizjikan, Thomas Shorter, Ana Töpf, Volker Straub, C. Marini Bettolo, Jordi Díaz‐Manera, Sophie Hambleton, Karin R. Engelhardt, Jill Clayton‐Smith, Siddharth Banka, Elizabeth Alexander, Adam Jackson, Laurence Faivre, Christel Thauvin, Antonio Vitobello, Anne‐Sophie Denommé‐Pichon, Yannis Duffourd, Ange‐Line Bruel, Christine Peyron, Aurore Pélissier, Sergi Beltrán, Marta Gut, Steven Laurie, Davide Piscia, Leslie Matalonga, Anastasios Papakonstantinou, Gemma Bullich, Alberto Corvò, Marcos Fernández-Callejo, Carles Hernandéz-Ferrer, Daniel Picó, Ida Paramonov, Hanns Lochmüller, Gulcin Gumus, Virginie Bros‐Facer, Ana Rath, Marc Hanauer, David Lagorce, Oscar Hongnat, Maroua Chahdil, Emeline Lebreton, Giovanni Stévanin, Alexandra Dürr, Claire-Sophie Davoine, Léna Guillot‐Noël, Anna Heinzmann, Giulia Coarelli, Gisèle Bonne, Teresinha Evangelista, Valérie Allamand, Isabelle Nelson, Rabah Ben Yaou, Corinne Métay, B. Eymard, Enzo Cohen, António Atalaia, Tanya Stojkovic, Milan Macek, Marek Turnovec, Dana Thomasová, Radka Pourová Kremliková, Věra Franková, Markéta Havlovicová, Petra Lišková, Pavla Doležalová, Helen Parkinson, Thomas Keane, Mallory Freeberg, Coline Thomas, Dylan Spalding, Peter N. Robinson, Daniel Daniš, Glenn Robert, Alessia Costa, Christine Patch, Mike Hanna, Henry Houlden, Mary M. Reilly, Jana Vandrovcová, Stéphanie Efthymiou, Heba Morsy, Elisa Calì, Francesca Magrinelli, Sanjay M. Sisodiya, Jonathan D. Rohrer, Francesco Muntoni, Irina Zaharieva, Anna Sárközy, Vincent Timmerman, Jonathan Baets, Geert de Vries, Jonathan De Winter, Danique Beijer, Peter De Jonghe, Liedewei Van de Vondel, Willem De Ridder, Sarah Weckhuysen, Vincenzo Nigro, Margherita Mutarelli, Manuela Morleo, Michele Pinelli, Alessandra Varavallo, Sandro Banfi, Annalaura Torella, Francesco Musacchia, Giulio Piluso, Alessandra Ferlini, Rita Selvatici, Francesca Gualandi, Stefania Bigoni, Rachele Rossi, Marcella Neri, Stefan Aretz, Isabel Spier, Anna Katharina Sommer, Sophia Peters, Carla Oliveíra, José 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, David Ruvolo, Kristin M. Abbott, Wilhemina S. Kerstjens Frederikse, Eveline Zonneveld-Huijssoon, Dieuwke Roelofs-Prins, Mariëlle van Gijn, Sebastian Köhler, Alison Metcalfe, Alain Verloès, Séverine Drunat, Delphine Héron, Cyril Mignot, Boris Keren, Jean‐Madeleine de Sainte Agathe, Caroline Rooryck, Didier Lacombe, Aurélien Trimouille, Manuel Posada de la Paz, Eva Bermejo, 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, Simone Furini, Chiara Fallerini, Elisa Benetti, Péter Balicza, Mária Judit Molnár, Aleš Maver, Borut Peterlin, Alexander Münchau, Katja Lohmann, Rebecca Herzog, Martje G. Pauly, Alfons Macaya, Ana Cazurro‐Gutiérrez, Belén Pérez‐Dueñas, Francina Munell, Clara Franco‐Jarava, Laura Batlle-Masó, Anna Marcé‐Grau, Roger Colobrán, A. Nascimento Osorio, Daniel Natera‐de Benito, Hanns Lochmüller, Rachel Thompson, Kiran Polavarapu, Bodo Grimbacher, David Beeson, Judith Cossins, Peter Hackman, Mridul Johari, Marco Savarese, Bjarne Udd, Rita Horváth, Patrick F. Chinnery, Thiloka Ratnaike, Fei Gao, Katherine Schon, Gabriel Capellá, Laura Valle, Elke Holinski‐Feder, Andreas Laner, Verena Steinke‐Lange, Evelin Schröck, Andreas Rump, A. Nazlı Başak, Dimitri Hemelsoet, Bart Dermaut, Nika Schuermans, Bruce Poppe, Hannah Verdin, Davide Mei, Annalisa Vetro, Simona Balestrini, Renzo Guerrini, Kristl G. Claeys, Gijs W.E. Santen, Emilia K. Bijlsma, Mariëtte J.V. Hoffer, Claudia Ruivenkamp, Kaan Boztuǧ, Matthias Haimel, Isabelle Maystadt, Isabelle Cordts, Marcus Deschauer, Ioannis Zaganas, Evgenia Kokosali, Mathioudakis Lambros, Athanasios Evangeliou, Martha Spilioti, Elisabeth Kapaki, Mara Bourbouli, Pasquale Striano, Federico Zara, Antonella Riva, Michele Iacomino, Paolo Uva, Marcello Scala, Paolo Scudieri, Maria-Roberta Cilio, Evelina Carpancea, Chantal Depondt, Damien Lederer, Yves Sznajer, Sarah Duerinckx, Sandrine Mary, Christel Depienne, Andreas Roos, Patrick May · 发表于：Human Genomics · 年份：2023 · DOI：10.1186/s40246-023-00485-5 · 被引用次数：33 · 研究领域：Genomics and Rare Diseases、Genomic variations and chromosomal abnormalities、Genomics and Phylogenetic Studies

BACKGROUND: Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS: We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION: We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.