CANOES: detecting rare copy number variants from whole exome sequencing data
Daniel Backenroth,Jason Homsy,Laura R. Murillo,J. Glessner,Edwin Lin,Martina Brueckner,Richard P. Lifton,Richard P. Lifton,Elizabeth Goldmuntz,Wendy K. Chung,Yufeng Shen +10 more
TL;DR: The CANOES method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER) and when used in combination with these methods will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data.
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Abstract: We present CANOES, an algorithm for the detection of rare copy number variants from exome sequencing data. CANOES models read counts using a negative binomial distribution and estimates variance of the read counts using a regression-based approach based on selected reference samples in a given dataset. We test CANOES on a family-based exome sequencing dataset, and show that its sensitivity and specificity is comparable to that of XHMM. Moreover, the method is complementary to Gaussian approximation-based methods (e.g. XHMM or CoNIFER). When CANOES is used in combination with these methods, it will be possible to produce high accuracy calls, as demonstrated by a much reduced and more realistic de novo rate in results from trio data.
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Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Qian Zhang,Paul Bastard,Paul Bastard,Zhiyong Liu,Jérémie Le Pen,Marcela Moncada-Vélez,Jie Chen,Masato Ogishi,Ira K. D. Sabli,Stephanie Hodeib,Cecilia B. Korol,Jérémie Rosain,Jérémie Rosain,Kaya Bilguvar,Junqiang Ye,Alexandre Bolze,Benedetta Bigio,Rui Yang,Andrés Augusto Arias,Andrés Augusto Arias,Qinhua Zhou,Yu Zhang,Fanny Onodi,Sarantis Korniotis,Léa Karpf,Quentin Philippot,Quentin Philippot,Marwa Chbihi,Marwa Chbihi,Lucie Bonnet-Madin,Karim Dorgham,Nikaïa Smith,William M. Schneider,Brandon S. Razooky,Hans-Heinrich Hoffmann,Eleftherios Michailidis,Leen Moens,Ji Eun Han,Lazaro Lorenzo,Lazaro Lorenzo,Lucy Bizien,Lucy Bizien,Philip Meade,Anna-Lena Neehus,Anna-Lena Neehus,Aileen Camille Ugurbil,Aurélien Corneau,Gaspard Kerner,Gaspard Kerner,Peng Zhang,Franck Rapaport,Yoann Seeleuthner,Yoann Seeleuthner,Jeremy Manry,Jeremy Manry,Cécile Masson,Yohann Schmitt,Agatha Schlüter,Tom Le Voyer,Tom Le Voyer,Taushif Khan,Juan Li,Jacques Fellay,Jacques Fellay,Lucie Roussel,Mohammad Shahrooei,Mohammed F. Alosaimi,Davood Mansouri,Haya Al-Saud,Fahd Al-Mulla,Feras M. Almourfi,Saleh Al-Muhsen,Fahad Alsohime,Saeed Al Turki,Rana Hasanato,Diederik van de Beek,Andrea Biondi,Laura Rachele Bettini,Mariella D'Angiò,Paolo Bonfanti,Luisa Imberti,Alessandra Sottini,Simone Paghera,Eugenia Quiros-Roldan,Camillo Rossi,Andrew J. Oler,Miranda F. Tompkins,Camille Alba,Isabelle Vandernoot,Jean-Christophe Goffard,Guillaume Smits,Isabelle Migeotte,Filomeen Haerynck,Pere Soler-Palacín,Andrea Martín-Nalda,Roger Colobran,Pierre-Emmanuel Morange,Sevgi Keles,Fatma Çölkesen,Tayfun Ozcelik,Kadriye Kart Yaşar,Sevtap Şenoğlu,Şemsi Nur Karabela,Carlos Rodríguez-Gallego,Giuseppe Novelli,Sami Hraiech,Yacine Tandjaoui-Lambiotte,Xavier Duval,Xavier Duval,Cédric Laouénan,Cédric Laouénan,Covid-Storm Clinicians§,Covid Clinicians,CoV-Contact Cohort§,CoV-Contact Cohort§,Amsterdam Umc Covid Biobank,Covid Human Genetic Effort,Niaid-Usuhs,Niaid-Usuhs,Niaid-Usuhs,Andrew L. Snow,Clifton L. Dalgard,Joshua D. Milner,Donald C. Vinh,Donald C. Vinh,Trine H. Mogensen,Trine H. Mogensen,Nico Marr,András N Spaan,András N Spaan,András N Spaan,Bertrand Boisson,Bertrand Boisson,Bertrand Boisson,Stéphanie Boisson-Dupuis,Jacinta Bustamante,Jacinta Bustamante,Jacinta Bustamante,Anne Puel,Michael J. Ciancanelli,Isabelle Meyts,Tom Maniatis,Vassili Soumelis,Ali Amara,Ali Amara,Michel C. Nussenzweig,Adolfo García-Sastre,Florian Krammer,Aurora Pujol,Darragh Duffy,Darragh Duffy,Richard P. Lifton,Richard P. Lifton,Richard P. Lifton,Shen-Ying Zhang,Guy Gorochov,Guy Gorochov,Guy Gorochov,Vivien Béziat,Vivien Béziat,Vivien Béziat,Emmanuelle Jouanguy,Vanessa Sancho-Shimizu,Charles M. Rice,Charles M. Rice,Charles M. Rice,Laurent Abel,Luigi D. Notarangelo,Luigi D. Notarangelo,Luigi D. Notarangelo,Aurélie Cobat,Helen C. Su,Jean-Laurent Casanova +172 more
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106
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92
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