21 research outputs found
Biomass and essential oil yields of cornmint (Mentha arvensis L.) grown in the irrigation area of Río Dulce, Santiago del Estero, Argentina.
- Author
- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2014
- Field of study
The aim of this study is to determine the yield and composition of the essential oil of cornmint (Mentha arvensis L.) grown in the irrigation area of Santiago del Estero, Argentina. Field tests were carried out under irrigation conditions, harvesting when 70% flowering was reached (in the summer and at the end of the winter seasons). Essential oil yields were 2% in the first cut and 1.6% in the second cut, respectively, the major constituents of the essential oil being menthol, menthone, isomenthone and menthofuran. In both cases, a high concentration of menthol was obtained, although during the winter the content decreased, increasing the concentration of menthofuran. It is concluded that during the summer a higher yield and better quality of essential oil are produced
Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases
- Author
- Alias Laura
- Arjona César
- Armstrong Judith
- Artuch R
- Aznar Gemma
- Baena Díez Neus
- Balcells Susanna
- Bayés Mònica
- Beltran Sergi
- Bernal Sara
- Blanco Ignacio
- Boronat Susana
- Bullich Gemma
- Calvo-Escalona Rosa
- Cantó Judith
- Capdevila Núria
- Cardellach Francesc
- Casasnovas Carlos
- Castellanos Elisabeth
- Costa Mar
- Cruz Jordi
- Cueto-González Anna
- Cusco Ivon
- Cáceres Alejandro
- Del Toro Mireia
- Diaz-Manera Jordi
- Fernández-Callejo Marcos
- Fusté Berta
- Gabau Elisabeth
- Gallano Pia
- Garcia-Garcia Francesc Josep
- Garcia-Villoria Judit
- García Belén
- García-Arumí Elena
- García-Cazorla Àngels
- Garrabou Glòria
- Gel Bernat
- González Juan R.
- González-Quereda Lídia
- Gort Laura
- Grinberg Daniel
- Guitart Míriam
- Gut Ivo
- Gut Marta
- Gómez-Andrés David
- Hernando-Davalillo Cristina
- Hernández-Ferrer Carles
- Laurie Steven
- Luengo Cristina
- Lázaro Conxi
- López-Grondona Fermina
- López-Sánchez Marcos
- Ma Grau Josep
- Macaya Ruiz Alfons
- Madrigal Irene
- Marcé-Grau Anna
- Martí Ramon
- Martínez-Monseny Antonio
- Matalonga Leslie
- Milisenda José César
- Milà Montserrat
- Munell Francina
- Muñoz-Cabello Patricia
- Muñoz-Pujol Gerard
- Nascimento Andrés
- Natera de Benito Daniel
- Olivé-Cirera Gemma
- Ortez Carlos
- Ovelleiro David
- Palau Francesc
- Papakonstantinou Anastasios
- Paramonov Ida
- Parra Genís
- Pelegrí-Sisó Dolors
- Picó Amador Daniel
- Piscia Davide
- Pujadas Montserrat
- Pujol Aurora
- Pérez-Dueñas Belén
- Pérez-Jurado Luis A.
- Rabionet Raquel
- Raspall-Chaure Miquel
- Ribes Antònia
- Rodriguez-Palmero Agustí
- Rodríguez-Revenga Laia
- Rojas-García Ricardo
- Romero Duque Penélope
- Ruiz Nel Lo Anna
- Sala-Coromina Júlia
- Schlüter Agatha
- Serrano Mercedes
- Spataro Nino
- Sànchez Aurora
- Tell Gemma
- Tizzano Eduardo
- Tobías Ester
- Tonda Raúl
- Tort Frederic
- Trotta Jean-Rémi
- Ugarteburu Olatz
- Universitat Autònoma de Barcelona
- Urreizti Roser
- Valenzuela Irene
- Vendrell Teresa
- Verdura Edgard
- Yubero Délia
- Álvarez-Mora Maria Isabel
- Publication venue
- Publication date
- 01/01/2022
- Field of study
Altres ajuts: Generalitat de Catalunya, Departament de Salut; Generalitat de Catalunya, Departament d'Empresa i Coneixement i CERCA Program; Ministerio de Ciencia e Innovación; Instituto Nacional de Bioinformática; ELIXIR Implementation Studies (CNAG-CRG); Centro de Investigaciones Biomédicas en Red de Enfermedades Raras; Centro de Excelencia Severo Ochoa; European Regional Development Fund (FEDER).Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%)
DMTs and Covid-19 severity in MS: a pooled analysis from Italy and France
- Author
- Abir Wahab
- Adil Maarouf
- Adrien Delourme
- Agnes Fromont
- Agostino Nozzolillo
- Alain Cr??ange
- Alain Cr??ange
- Alberto Gajofatto
- Alessandra Bellacosa
- Alessandra Protti
- Alessandro d'Ambrosio
- Alessandro Marti
- Alessia d'Arma
- Alessia Di Sapio
- Alessia Sartori
- Alessio Signori
- Alexis Montcuquet
- Alfredo Petrone
- Alvino Bisecco
- Amandine Bordet
- Anastasia Alteno
- Angelica Guareschi
- Aniello Iovino
- Anna Dutto
- Anna Ghazaryan
- Anna M Pietroboni
- Anna Palmieri
- Anna Repice
- Anne Kerbrat
- Anne???Laure Dubessy
- Anne???Marie Guennoc
- Antoine Gueguen
- Antonella Conte
- Antonio Bosco
- Antonio Gallo
- Antonio Ianniello
- Antonio Zito
- Ari??le Azoulay???Cayla
- Arianna Sartori
- Arnaud Gagnol
- Arnaud Kwiatkowski
- Aude Maurousset
- Audrey Rico
- Aur??lie Ruet
- Aurelian Ungureanu
- Aurore Jourdain
- Ayman Tourbah
- Beatrice Biolzi
- Beatrice Maria Allegri Rossi
- Benedetta Bodini
- Bertrand Audoin
- Bertrand Bourre
- Bruno Brochet
- Bruno Giometto
- Bruno Stankoff
- Bruno Stankoff
- C??line Louapre
- Camille Rizzato
- Carla Tortorella
- Carlo Antozzi
- Carlo Piantadosi
- Carlo Pozzilli
- Carolina Gabri Nicoletti
- Caroline Bensa
- Caroline Bensa???Koscher
- Caroline Papeix
- Caroline Pot
- Catalina Coclitu
- Caterina Barril??
- Caterina Lapucci
- Caterina Sgarito
- Catherine Lubetzki
- Cecile Dulau???Metras
- Celine Louapre
- Chiara Bosa
- Chiara Rosa Mancinelli
- Christian Cordano
- Christine Clerc
- Christine Lebrun???Frenay
- Cinzia Cordioli
- Cinzia Cordioli
- Cinzia Scandellari
- Cl??mence Boutiere
- Claire Giannesini
- Clara Chisari
- Clara Guaschino
- Clarisse Carra???Dalliere
- Claudio Correale
- Claudio Gasperini
- Claudio Solaro
- Cristina Fioretti
- Daiana Bezzini
- Dalia Dimitri
- Damiano Baroncini
- Damiano Marastoni
- Damiano Paolicelli
- Damien Biotti
- Dan Buch
- Daniele Imperiale
- David Laplaud
- Davide Maimone
- Diana Ferraro
- Dominique Audry
- Domizia Vecchio
- Donata Guidetti
- Doriana Landi
- Dorothee Videt
- Edouard Januel
- Eduardo Nobile???Orazio
- Eleonora Cocco
- Eleonora Rigoni
- Eleonora Virgilio
- Elisabeth Maillart
- Elisabetta Bucciantini
- Elisabetta Pedrazzoli
- Elisabetta Signoriello
- Elvira Sbragia
- Emanuela Laura Susani
- Emanuele D'Amico
- Emilio Portaccio
- Emmanuelle Page
- Eric Berger
- Eric Manchon
- Eric Thouvenot
- Eric Thouvenot
- Erica Curti
- Erica Grange
- Eva Milano
- Evelyne Planque
- Fabiana Marinelli
- Fay??al Derouiche
- Federco Masserano Zoli
- Federica Pinardi
- Federico Camilli
- Federico Montini
- Filippo Martinelli Boneschi
- Flora Govone
- Flora Lejeune
- Fr??d??ric Taithe
- Fran??oise Durand???Dubief
- Francesca Bovis
- Francesca Calabria
- Francesca Caleri
- Francesca Gobbin
- Francesca Matta
- Francesca Rinaldi
- Francesca Ruscica
- Francesca Sireci
- Francesca Vitetta
- Francesco Corea
- Francesco Crescenzo
- Francesco Patti
- Francesco Patti
- Francesco Teatini
- Franco Granella
- Francois Sellal
- Frederique Le Breton
- G??raldine Androdias???Condemine
- Gabriele Siciliano
- Gabriella Turano
- Gaia Cola
- Giacomo Lus
- Giampaolo Brichetto
- Giancarlo Comi
- Giancarlo Comi
- Gianmarco Abbadessa
- Gianmarco Bellucci
- Gilles Defer
- Gilles Edan
- Gioacchino Tedeschi
- Gioacchino Tedeschi
- Giorgia Teresa Maniscalco
- Giovanna Borriello
- Giovanna De Luca
- Giovanna Konrad
- Giovanna Vaula
- Giovanni Castelnovo
- Girolama Alessandra Marfia
- Giuditta Ilaria Scarano
- Giulia Mallucci
- Giulietta Tabiadon
- Giuseppe Liberatore
- Giuseppe Meucci
- Giuseppe Salemi
- Giuseppina Miele
- Grazia Sibilia
- Guido Ahle
- Guillaume Mathey
- Helene Zephir
- Helene Zephir
- Herv?? Fayolle
- Ignazio Roberto Zarbo
- Ilaria Pesci
- Ionescu Iuliana
- Irene Schiavetti
- Irene Schiavetti
- J??r??me De S??ze
- J??r??mie Papassin
- Jean Capron
- Jean Christophe Corvol
- Jean Christophe Seghezzi
- Jean Pelletier
- Jean Pelletier
- Jean???Christophe Ouallet
- Jean???Philippe Neau
- Jennifer Aboab
- Jerome De Seze
- Jerome Grimaud
- Jessica Frau
- Jonathan Ciron
- Jonathan Ciron
- Julie Boucher
- Julie Pique
- Julien Poupart
- Karine Mougine
- Kevin Bigaut
- Kumaran Deiva
- Laura Brambilla
- Laura Mendozzi
- Laure Michel
- Laurent Guilloton
- Laurent Kremer
- Leonardo Lopiano
- Leonardo Sinisi
- Lia Allegorico
- Livia Pasquali
- Loredana Sabattini
- Lorena Lorefice
- Lorenzo Saraceno
- Luana Evangelista
- Luca Carmisciano
- Luca Carmisciano
- Luca Mancinelli
- Luca Prosperini
- Lucia Appendino
- Lucia Moiola
- Lucia Moiola
- Lucile Gleyze
- Luigi Iasevoli
- Luigi Lavorgna
- Luigi Zuliani
- Luisa Maria Caniatti
- Luisa Past??
- Maddalena Sparaco
- Magalie Rabin
- Marc Coustans
- Marc Debouverie
- Marcello Calogero Romano
- Marcello Moccia
- Marco Bozzali
- Marco Capobianco
- Marco Capobianco
- Marco Della Cava
- Marco Longoni
- Marco Onofrj
- Marco Ronzoni
- Marco Rovaris
- Marco Salvetti
- Marco Salvetti
- Marco Vercellino
- Margherita Monti Bragadin
- Maria Buccafusca
- Maria Cellerino
- Maria Chiara Buscarinu
- Maria Grazia Celani
- Maria Grazia Grasso
- Maria Laura Stromillo
- Maria Malentacchi
- Maria Paola Cabboi
- Maria Petracca
- Maria Pia Amato
- Maria Pia Sormani
- Maria Pia Sormani
- Maria Rita L'Episcopo
- Maria Sessa
- Maria Teresa Ferr??
- Maria Teresa Infante
- Maria Teresa Rilla
- Maria Trojano
- Maria Trojano
- Maria Trotta
- Marianna Lo Re
- Marie Th??audin
- Marie Th??audin
- Marie???celine Fleury
- Marika Vianello
- Marinella Clerico
- Mario A Battaglia
- Mario Alberto Battaglia
- Mario di Napoli
- Mario Fratta
- Marta Ponzano
- Marta Radaelli
- Marta Radaelli
- Marta Zaffira Conti
- Marzia Fronza
- Massimiliano Calabrese
- Massimiliano Mirabella
- Massimo Filippi
- Mathieu Vaillant
- Mathilde Goudot
- Matilde Inglese
- Matteo Lucchini
- Mattia Pozzato
- Maud Pallix???Guyot
- Maura Chiara Danni
- Mauro Zaffaroni
- Mauro Zampolini
- Maya Tchikviladze
- Michella Ibrahim
- Micka??l Zedet
- Mikael Cohen
- Monica Ulivelli
- Nathalie Derache
- Nicola De Rossi
- Nicola De Rossi
- Nicola De Stefano
- Nicolas Collongues
- Nicolas Maubeuge
- Olivier Casez
- Olivier Casez
- Olivier Gout
- Olivier Heinzlef
- Ombline Fagniez
- Paola Cavalla
- Paola Perini
- Paolo Confalonieri
- Paolo De Mitri
- Paolo Gallo
- Paolo Immovilli
- Paolo Immovilli
- Paolo Manganotti
- Paolo Ragonese
- Patrick Hautecoeur
- Patrick Vermersch
- Patrizia Carta
- Patrizia Sola
- Pekes Codjia
- Philippe Kerschen
- Philippe Kerschen
- Pierre Branger
- Pierre Clavelou
- Pierre Clavelou
- Pierre Labauge
- Pierre Labauge
- Pierre Yves Garcia
- Pietro Annovazzi
- Pietro Iaffaldano
- Raffaele Nardone
- Raffaella Cerqua
- Raffaella Clerici
- Rana Assouad
- Raphael De Paz
- Renato Docimo
- Renaud Du Pasquier
- Riccardo Orlandi
- Roberta Lanzillo
- Roberta Motta
- Roberto Balgera
- Roberto Bergamaschi
- Roberto Cantello
- Rocco Capuano
- Rocco Totaro
- Romain Deschamps
- Romain Marignier
- Rosa Iodice
- Rosanna Missione
- Ruggero Capra
- Sabrina Marangoni
- Sabrina Realmuto
- Salimata Gassama
- Salvatore Cottone
- Salvatore Fanara
- Samar S Ayache
- Sandra Vukusic
- Sandra Vukusic
- Sandrine Wiertlewski
- Sara Montepietra
- Sarah Coulette
- Sarah Demorti??re
- Sarah Rasia
- Saskia Bresch
- Sebastiano Arena
- Sebastiano Bucello
- Serena Leva
- Silvia Miante
- Silvia Strumia
- Simona Bonavita
- Simona Malucchi
- Simona Toscano
- Simone Guerrieri
- Simone Tonietti
- Sinead Zeidan
- Sophie Pittion
- St??phane Beltran
- Stefania Federica De Mercanti
- Stefano Biase
- Stefano Sotgiu
- Stefano Vollaro
- Susanna Cordera
- Thibault Moreau
- Thibault Moreau
- Thomas Roux
- Umberto Aguglia
- V??ronique Marcaud
- Valentina Scarano
- Valentina Tomassini
- Valentina Torri Clerici
- Valentino Manzo
- Valeria Barcella
- Valeria Bergamaschi
- Vincenzo Brescia Morra
- Vincenzo Dattola
- Viola Baione
- Vito A. G Ricigliano
- Vittorio Mantero
- Xavier Ayrignac
- Xavier Moisset
- Yanica Mathieu
- Ysoline Beigneux
- Publication venue
- 'Wiley'
- Publication date
- 01/01/2021
- Field of study
We evaluated the effect of DMTs on Covid-19 severity in patients with MS, with a pooled-analysis of two large cohorts from Italy and France. The association of baseline characteristics and DMTs with Covid-19 severity was assessed by multivariate ordinal-logistic models and pooled by a fixed-effect meta-analysis. 1066 patients with MS from Italy and 721 from France were included. In the multivariate model, anti-CD20 therapies were significantly associated (OR = 2.05, 95%CI = 1.39–3.02, p < 0.001) with Covid-19 severity, whereas interferon indicated a decreased risk (OR = 0.42, 95%CI = 0.18–0.99, p = 0.047). This pooled-analysis confirms an increased risk of severe Covid-19 in patients on anti-CD20 therapies and supports the protective role of interferon
Twist exome capture allows for lower average sequence coverage in clinical exome sequencing
- Author
- Abbott Kristin M.
- Alexander Elizabeth
- Allamand Valérie
- Aretz Stefan
- Atalaia Antonio
- Baets Jonathan
- Balestrini Simona
- Balicza Peter
- Banfi Sandro
- Banka Siddharth
- Başak Ayşe Nazlı
- Beeson David
- Beijer Danique
- Beltran Sergi
- Benetti Elisa
- Bettolo Chiara Marini
- Bigoni Stefania
- Bijlsma Emilia K.
- Bonne Gisèle
- Bourbouli Mara
- Boztug Kaan
- Brookes Anthony J.
- Bros-Facer Virginie
- Bruel Ange-Line
- Brunner Han
- Bullich Gemma
- Cali Elisa
- Capella Gabriel
- Carneiro Fátima
- Carpancea Evelina
- Cazurro-Gutiérrez Ana
- Chahdil Maroua
- Chinnery Patrick F.
- Cilio Maria-Roberta
- Ciolfi Andrea
- Claeys Kristl
- Clayton-Smith Jill
- Coarelli Giulia
- Cohen Enzo
- Colobran Roger
- consortium Solve-R. D.
- Cordts Isabelle
- Corominas Galbany Jordi
- Corvo Alberto
- Cossins Judith
- Costa Alessia
- Dallapiccola Bruno
- Danis Daniel
- Davoine Claire-Sophie
- de Benito Daniel Natera
- de Boer Elke
- de Jonghe Peter
- De la Paz Manuel Posada
- de la Rosa F. Javier Alonso García
- De Ridder Willem
- de Sainte Agathe Jean-Madeleine
- de Voer Richarda M.
- de Vries Geert
- De Winter Jonathan
- Delgado Beatriz Martínez
- Demidov German
- Denommé-Pichon Anne-Sophie
- Depienne Christel
- Depondt Chantal
- Dermaut Bart
- Deschauer Marcus
- Dizjikan Farid Yavari
- Doležalová Pavla
- Drunat Séverine
- Duerinckx Sarah
- Duffourd Yannis
- Durr Alexandra
- Efthymiou Stephanie
- Ellwanger Kornelia
- Engelhardt Karin
- Evangeliou Athanasios
- Evangelista Teresinha
- Eymard Bruno
- Faivre Laurence
- Fallerini Chiara
- Ferlini Alessandra
- Fernandes Susana
- Fernandez-Callejo Marcos
- Ferreira Marta
- Ferreira Pedro
- Franková Vera
- Frederikse Wilhemina Skerstjens
- Freeberg Mallory
- Furini Simone
- Gao Fei
- Garrido Luzia
- Gibson Spencer
- Gilissen Christian
- Gilissen Christian
- Graessner Holm
- Grimbacher Bodo
- Gualandi Francesca
- Guerrini Renzo
- Guillot-Noel Léna
- Gullo Irene
- Gumus Gulcin
- Gut Ivo Glynne
- Haack Tobias B.
- Hackman Peter
- Haimel Matthias
- Hambleton Sophie
- Hampstead Juliet
- Hanauer Marc
- Hanna Mike
- Havlovicová Markéta
- Heinzmann Anna
- Hemelsoet Dimitri
- Hengel Holger
- Hernández Carles
- Heron Delphine
- Herzog Rebecca
- Heutink Peter
- Hoen Peter A. C. T
- Hoffer Mariette J. V.
- Hofste Tom
- Hoischen Alexander
- Hoischen Alexander
- Holinski-Feder Elke
- Hongnat Oscar
- Hoogerbrugge Nicoline
- Horvath Rita
- Houlden Henry
- Iacomino Michele
- Jackson Adam
- Janssen Erik
- Jarava Clara Franco
- Johansson Lennart
- Johari Mridul
- José Celina São
- Kamsteeg Erik-Jan
- Kapaki Elisabeth
- Keane Thomas
- Kegele Josua
- Keren Boris
- Kessler Christoph
- Kleefstra Tjitske
- Kokosali Evgenia
- Kremliková Radka Pourová
- Kucuk Erdi
- Köhler Sebastian
- Lacombe Didier
- Lagorce David
- Lambros Mathioudakis
- Laner Andreas
- Laurie Steven
- Lebreton Emeline
- Lederer Damien
- Lerche Holger
- Lišková Petra
- Lochmüller Hanns
- Lochmüller Hanns
- Lohmann Katja
- Macaya Alfons
- Macek Milan
- Maddi Vatsalya
- Magrinelli Francesca
- Manera Jordi Diaz
- Marcé-Grau Anna
- Martín Estrella López
- Mary Sandrine
- Masó Laura Batlle
- Matalonga Leslie
- Matos Ana Rita
- Maver Ales
- May Patrick
- Maystadt Isabelle
- Mehtarizadeh Mehdi
- Mei Davide
- Metay Corinne
- Metcalfe Alison
- Mignot Cyril
- Molnar Maria Judit
- Morleo Manuela
- Morsy Heba
- Munell Francina
- Muntoni Francesco
- Musacchia Francesco
- Mutarelli Margherita
- Münchau Alexander
- Neerincx Pieter B.
- Nelen Marcel
- Nelson Isabelle
- Neri Marcella
- Nigro Vincenzo
- Oliveira Carla
- Osorio Andrés Nascimento
- Ossowski Stephan
- Papakonstantinou Anastasios
- Paramonov Ida
- Parkinson Helen
- Patch Christine
- Pauly Martje
- Pelaez Jose Garcia
- Peterlin Borut
- Peters Sophia
- Peyron Christine
- Pfundt Rolph
- Picó Daniel
- Piluso Giulio
- Pinelli Michele
- Piscia Davide
- Pizzi Simone
- Polavarapu Kiran
- Poppe Bruce
- Pélissier Aurore
- Pérez-Dueñas Belén
- Radio Francesca Clementina
- Rath Ana
- Ratnaike Thiloka
- Reilly Mary
- Renieri Alessandra
- Riaz Umar
- Riess Olaf
- Rinne Tuula
- Riva Antonella
- Robert Glenn
- Robinson Peter
- Roelofs-Prins Dieuwke
- Rohrer Jonathan
- Rooryck Caroline
- Roos Andreas
- Rossi Rachele
- Ruivenkamp Claudia A. L.
- Rump Andreas
- Ruvolo David
- Sablauskas Karolis
- Santen Gijs W. E.
- Sarkozy Anna
- Savarese Marco
- Scala Marcello
- Scheffer Hans
- Schon Katherine
- Schröck Evelin
- Schuermans Nika
- Schulze-Hentrich Julia M.
- Schöls Ludger
- Schüle Rebecca
- Scudieri Paolo
- Selvatici Rita
- Shorter Thomas
- Sisodiya Sanjay M.
- Sommer Anna Katharina
- Spalding Dylan
- Spier Isabel
- Spilioti Martha
- Steehouwer Marloes
- Steinke-Lange Verena
- Stevanin Giovanni
- Steyaert Wouter
- Stojkovic Tanya
- Straub Volker
- Striano Pasquale
- Sturm Marc
- Swertz Morris A.
- Synofzik Matthis
- Sznajer Yves
- Sánchez Eva Bermejo
- Tartaglia Marco
- te Paske Iris
- Thauvin Christel
- Thomas Coline
- Thomasová Dana
- Thompson Rachel
- Timmerman Vincent
- Torella Annalaura
- Traschütz Andreas
- Trimouille Aurelien
- Turnovec Marek
- Töpf Ana
- Udd Bjarne
- Uva Paolo
- Valle Laura
- Van de Vondel Liedewei
- van de Warrenburg Bart
- van der Velde Joeri K.
- van der Vries Gerben
- van Gijn Marielle
- van Os Nienke
- Vandrovcova Jana
- Varavallo Alessandra
- Veal Colin
- Verdin Hannah
- Verloes Alain
- Vetro Annalisa
- Vissers Lisenka E. L. M.
- Vitobello Antonio
- Warren Greg
- Wayand Melanie
- Weckhuysen Sarah
- Wilke Carlo
- Xu Jishu
- Yaldiz Burcu
- Yaldiz Burcu
- Yaou Rabah Ben
- Yntema Helger G.
- Zaganas Ioannis
- Zaharieva Irina
- Zara Federico
- Zonneveld-Huijssoon Eveline
- Zurek Birte
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2023
- Field of study
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
A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing
- Author
- Abbott Kristin M.
- Abbott Kristin M.
- Afenjar Alexandra
- Agathe Jean-Madeleine de Sainte
- Agathe Jean-Madeleine de Sainte
- Albuisson Juliette
- Alembik Yves
- Alessandri Jean-Luc
- Alexander Elizabeth
- Allamand Valérie
- Alonso García de la Rosa F. Javier
- Amiel Jeanne
- Amram Daniel
- Aretz Stefan
- Atalaia Antonio
- Attie-Bitach Tania
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- Başak Ayşe Nazlı
- Beeson David
- Beijer Danique
- Bellanger Séverine Audebert
- Beltran Sergi
- Ben Yaou Rabah
- Benetti Elisa
- Benetti Elisa
- Bettolo Chiara Marini
- Bigoni Stefania
- Bitoun Pierre
- Bizaoui Varoona
- Blesson Sophie
- Boer Elke de
- Bongers Ernie
- Bonne Gisèle
- Bonnet-Dupeyron Marie Noëlle
- Bonniaud Bertille
- Bourbouli Mara
- Bournez Marie
- Boute Odile
- Boztug Kaan
- Brookes Anthony J.
- Bros-Facer Virginie
- Bruel Ange-Line
- Bruel Ange-Line
- Brunner Han
- Bullich Gemma
- Busa Tiffany
- Cali Elisa
- Capella Gabriel
- Capri Yline
- Carneiro Fátima
- Carpancea Evelina
- Cartault François
- Cazurro-Gutiérrez Ana
- Chahdil Maroua
- Chassaing Nicolas
- Chiaverini Christine
- Chinnery Patrick F.
- Cilio Maria-Roberta
- Ciolfi Andrea
- Ciolfi Andrea
- Ciolfi Andrea
- Claeys Kristl
- Clayton-Smith Jill
- Clayton-Smith Jill
- Clayton-Smith Jill
- Coarelli Giulia
- Cohen Enzo
- Cohen Enzo
- Colin Estelle
- Colobran Roger
- Colson Cindy
- Cordier-Alex Marie-Pierre
- Cordts Isabell
- Corvo Alberto
- Cossins Judith
- Costa Alessia
- Coubes Christine
- Cusin Véronica
- Dallapiccola Bruno
- Dallapiccola Bruno
- Dallapiccola Bruno
- Danis Daniel
- Danis Daniel
- Davoine Claire-Sophie
- de Boer Elke
- de Boer Elke
- de Boer Elke
- de Jonghe Peter
- De la Paz Manuel Posada
- De Ridder Willem
- de Voer Richarda M.
- de Vries Bert B.A.
- de Vries Geert
- De Winter Jonathan
- Delanne Julian
- Delgado Beatriz Martínez
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- Denommé-Pichon Anne-Sophie
- Denommé-Pichon Anne-Sophie
- Denommé-Pichon Anne-Sophie
- Depienne Christel
- Depondt Chantal
- Dermaut Bart
- Deschauer Marcus
- Desplantes Claire
- Diene Gwenaëlle
- Dieux-Coeslier Anne
- Dizjikan Farid Yavari
- Doco-Fenzy Martine
- Doležalová Pavla
- Doray Bérénice
- Drouin-Garraud Valérie
- Drunat Séverine
- Duerinckx Sarah
- Duffourd Yannis
- Duffourd Yannis
- Durr Alexandra
- Efthymiou Stephanie
- El Chehadeh Salima
- Ellwanger Kornelia
- Ellwanger Kornelia
- Engelhardt Karin
- Evangeliou Athanasios
- Evangelista Teresinha
- Eymard Bruno
- Faivre Laurence
- Faivre Laurence
- Faivre Laurence
- Fallerini Chiara
- Fallerini Chiara
- Fargeot Anne
- Feillet François
- Ferlini Alessandra
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- Graessner Holm
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- Haack Tobias B.
- Haack Tobias B.
- Haack Tobias B.
- Hackman Peter
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- Nelson Isabelle
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- Posada Manuel
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- Riess Olaf
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- Robinson Peter
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- Rooryck Caroline
- Rooryck Caroline
- Rooryck Caroline
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- Rossi Rachele
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- Ruivenkamp Claudia A.L.
- Rump Andreas
- Ruvolo David
- Ryba Lukas
- Ryba Lukas
- Sablauskas Karolis
- Safraou Hana
- Samimi Mahtab
- Sanlaville Damien
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- Sarda Pierre
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- Savarese Marco
- Scala Marcello
- Schaefer Élise
- Scheffer Hans
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- Schröck Evelin
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- Schulze-Hentrich Julia M.
- Schwarz Martin
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- Schöls Ludger
- Schüle Rebecca
- Scudieri Paolo
- Selvatici Rita
- Shorter Thomas
- Sisodiya Sanjay M.
- Sommer Anna Katharina
- Sorlin Arthur
- Spalding Dylan
- Spier Isabel
- Spilioti Martha
- Spodenkiewicz Marta
- Steehouwer Marloes
- Steichen Elisabeth
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- Steyaert Wouter
- Steyaert Wouter
- Stojkovic Tanya
- Straub Volker
- Striano Pasquale
- Sturm Marc
- Swertz Morris A.
- Synofzik Matthis
- Sznajer Yves
- Sánchez Eva Bermejo
- Tartaglia Marco
- Tartaglia Marco
- Tartaglia Marco
- te Paske Iris B.A.W.
- Thauvin Christel
- Thauvin Christel
- Thauvin-Robinet Christel
- Thevenon Julien
- Thomas Coline
- Thomasová Dana
- Thompson Rachel
- Timmerman Vincent
- Torella Annalaura
- Torella Annalaura
- Touraine Renaud
- Toutain Annick
- Tran Mau-Them Frédéric
- Traschütz Andreas
- Trimouille Aurelien
- Trimouille Aurélien
- Trimouille Aurélien
- Trimouille Aurélien
- Turnovec Marek
- Töpf Ana
- Töpf Ana
- Udd Bjarne
- Uva Paolo
- Vabres Pierre
- Valle Laura
- Van de Vondel Liedewei
- van de Warrenburg Bart
- van der Velde Joeri K.
- van der Velde Joeri K.
- van der Vries Gerben
- van Gijn Marielle
- Van Kien Philippe Khau
- Van Maldergem Lionel
- van Os Nienke
- Vandrovcova Jana
- Vandrovcova Jana
- Varavallo Alessandra
- Veal Colin
- Verdin Hannah
- Verloes Alain
- Verloes Alain
- Verloes Alain
- Vetro Annalisa
- Vincent Marie
- Vincent-Delorme Catherine
- Vissers Lisenka
- Vissers Lisenka E.L.M.
- Vissers Lisenka E.L.M.
- Vitobello Antonio
- Vitobello Antonio
- Vitobello Antonio
- Vitobello Antonio
- Votypka Pavel
- Votypka Pavel
- W.E Gijs
- Warren Greg
- Wayand Melanie
- Weckhuysen Sarah
- Wells Constance
- Whalen Sandra
- Wilke Carlo
- Willems Marjolaine
- Willemsen Marjolein H.
- Xu Jishu
- Yaldiz Burcu
- Zaganas Ioannis
- Zaharieva Irina
- Zara Federico
- Zguro Kristina
- Zivi Einat
- Zonneveld-Huijssoon Eveline
- Zurek Birte
- Zurek Birte
- ‘t Hoen Peter A.C.
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2023
- Field of study
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
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- A Gordon Robertson
- Abdullah Kahraman
- Abel Gonzalez-Perez
- Adam A Margolin
- Adam Abeshouse
- Adam Grundhoff
- Adam J Struck
- Adam J Struck
- Adam J Wright
- Adam Lambert
- Adam P Butler
- Adam P Butler
- Adel El-Naggar
- Adnan M Nagrial
- Adrian Ally
- Adrian Baez-Ortega
- Adrian Thorogood
- Adriana Salcedo
- Adrienne M Flanagan
- Ake Borg
- Akihiro Fujimoto
- Akihiro Suzuki
- Akinyemi I Ojesina
- Alain Viari
- Alan J Robertson
- Alan P Hoyle
- Alan Thompson
- Alasdair Stenhouse
- Alastair M Thompson
- Aldo Scarpa
- Alessandro Pastore
- Alex Buchanan
- Alex Buchanan
- Alexander Claviez
- Alexander J Lazar
- Alexander Martinez-Fundichely
- Alfonso Muñoz
- Alfonso Valencia
- Aliaksei Z Holik
- Alice Meng
- Alicia L Bruzos
- Allison Creason
- Allison P Heath
- Alvin Wei Tian Ng
- Alvis Brazma
- Amaro Taylor-Weiner
- Amber L Johns
- Amie Radenbaugh
- Amit G Deshwar
- Ana Dueso-Barroso
- Ana Mijalkovic Mijalkovic-Lazic
- Ana Milovanovic
- Ana Milovanovic
- Andre Kahles
- Andrea Haake
- Andrea Holbrook
- Andrea L Richardson
- Andrea Mafficini
- Andrea Ruzzenente
- Andreas Behren
- Andreas Rosenwald
- Andreia V Pinho
- Andrew Berchuck
- Andrew D Cherniack
- Andrew J Dunford
- Andrew J Mungall
- Andrew J Spillane
- Andrew Menzies
- Andrew Menzies
- Andrew P Barbour
- Andrew Tutt
- Andrew V Biankin
- Andrey Korshunov
- Andrés Lanzós
- Andy Cafferkey
- Andy G Lynch
- Angela Chou
- Angela N Brooks
- Angela Tam
- Angelica Ochoa
- Angelika N Christ
- Angelo P Dei Tos
- Anieta M Sieuwerts
- Anil K Sood
- Anita Langerød
- Anja Füllgrabe
- Anke K Bergmann
- Ann-Marie Patch
- Anna deFazio
- Anna Ehinger
- Anna Fitzgerald
- Anne Hamilton
- Anne Vincent-Salomon
- Anne Y Warren
- Anne-Lise Børresen-Dale
- Annegien Broeks
- Anthony DiBiase
- Anthony J Gill
- Anthony Ng
- Anthony R Green
- Antonia L Pritchard
- Antonio Pea
- Antonios Koures
- Aparna Prasad
- Apurva M Hegde
- Aquila Fatima
- Arcadi Navarro
- Arie B Brinkman
- Arif O Harmanci
- Arindam Maitra
- Armando Lopez-Guillermo
- Arndt Borkhardt
- Arnoud Boot
- Asger Hobolth
- Ashley Williams
- Ashton A Connor
- Atul J Butte
- Aurélien Chateigner
- Austin J Hepperla
- Axel Aretz
- Aya Sasaki-Oku
- Ayellet V Segre
- B F Francis Ouellette
- Bailey Matthew H
- Barbara Hutter
- Barbara Hutter
- Barbara Kremeyer
- Bartha M Knoppers
- Beifang Niu
- Beifang Niu
- Beifang Niu
- Benedikt Brors
- Benita Kiat Tee Tan
- Benjamin J Raphael
- Benjamin P Berman
- Benjamin Raeder
- Bernardo Rodriguez-Martin
- Bernhard Radlwimmer
- Bernice H Wong
- Beth Karlan
- Bin Tean Teh
- Bin Zhu
- Birgit Burkhardt
- Bishoy M Faltas
- Bodil Bjerkehagen
- Bogdan Czerniak
- Boris Winterhoff
- Borislav C Rusev
- Bradly G Wouters
- Brandi N Davis-Dusenbery
- Brian Craft
- Brian D O'Connor
- Brian Patrick O'Neill
- Brice Aminou
- Calvin Wing Yiu Chan
- Cameron M Soulette
- Carl Herrmann
- Carl Morrison
- Carlo Gambacorti-Passerini
- Carlos Caldas
- Carlos D Bustamante
- Carlos López-Otín
- Carlota Rubio-Perez
- Carmen Gomez
- Carolien H M van Deurzen
- Carolyn M Hutter
- Carolyn M Hutter
- Carrie Cibulskis
- Caterina Vicentini
- Catherine A Shang
- Catherine D Moser
- Catherine J Kennedy
- Catrina C Fronick
- Chad J Creighton
- Chandra Sekhar Pedamallu
- Chang Li
- Charles David Imbusch
- Charles M Perou
- Charles Saller
- Charles Short
- Charlie E Massie
- Chawalit Pairojkul
- Chen Hong
- Chen Ye
- Cheng-Zhong Zhang
- Chin-Lee Wu
- Chip Stewart
- Chip Stewart
- Chip Stewart
- Choon Kiat Ong
- Chris Lawerenz
- Chris Mitchell
- Chris Sander
- Christian von Mering
- Christiane Buchholz
- Christina K Yung
- Christina K Yung
- Christina Yau
- Christine A Iacobuzio-Donahue
- Christine Chomienne
- Christine Desmedt
- Christine P'ng
- Christof von Kalle
- Christoph Borst
- Christoph Plass
- Christopher A Miller
- Christopher Benz
- Christopher J Scarlett
- Christopher J Yoon
- Christopher K Wong
- Christopher M Lalansingh
- Christopher M Lalansingh
- Christopher Ogden
- Christopher S Foster
- Christopher Umbricht
- Christopher W Toon
- Christos Sotiriou
- Cindy Bell
- Cinzia Cantù
- Ciyue Shen
- Claes Wadelius
- Clare Verrill
- Clarissa Gerhauser
- Claudia Calabrese
- Claudio Bassi
- Claudio Luchini
- Claudiu Farcas
- Clemency Jolly
- Colin A Purdie
- Colin A Semple
- Colin C Collins
- Colin S Cooper
- Conrad R Leonard
- Constance H Li
- Corbin D Jones
- Craig Shriver
- Cristina López
- Cyriac Kandoth
- Cyril Fisher
- D Neil Hayes
- Dai-Ying Wu
- Daiming Fan
- Daisuke Komura
- Dale W Garsed
- Daniel A Leongamornlert
- Daniel Baumhoer
- Daniel Hübschmann
- Daniel J Turner
- Daniel J Weisenberger
- Daniel M Berney
- Daniel Rosebrock
- Daniel S Brewer
- Daniela S Gerhard
- Danielle Pasternack
- Darell Bigner
- Dariush Etemadmoghadam
- Darlene Lee
- Darrin F Taylor
- Dave Larson
- David A Wheeler
- David A Wheeler
- David C Wedge
- David Craft
- David D L Bowtell
- David E Neal
- David Haan
- David Haussler
- David Haussler
- David Hedley
- David Huntsman
- David I Heiman
- David J Adams
- David J Van Den Berg
- David K Chang
- David K Miller
- David Khoo
- David Mutch
- David N Louis
- David Nicol
- David Ocana
- David R Jones
- David R Jones
- David Scott
- David T Bowen
- David T W Jones
- David Tamborero
- David Torrents
- David Torrents
- David Townend
- David Vicente
- Davide Antonello
- Declan Cahill
- Denis Larsimont
- Denis Yuen
- Denise Brooks
- Deniz Demircioğlu
- Dennis C Sgroi
- Dennis Karsch
- Dennis T Maglinte
- Dennis Wigle
- Derek W Wright
- Dianne E Chadwick
- Dido Lenze
- Dieter Kube
- Dieter Weichenhan
- Dilip D Giri
- Dimitri Livitz
- Dimitri Livitz
- Dimple Chakravarty
- Ding
- Dirk Schadendorf
- Dmitry A Gordenin
- Dominik Glodzik
- Don Chalmers
- Dong Guanlan
- Dongbing Liu
- Donghoon Lee
- Donghui Tan
- Donna M Muzny
- Dorthe Grabau
- Douglas A Levine
- Douglas F Easton
- Douglas Voet
- Duncan Beardsmore
- Dursi Lewis Jonathan
- Edward W Rowe
- Eigo Shimizu
- Ekta Khurana
- Elaine R Mardis
- Electron Kebebew
- Elena Piñeiro-Yáñez
- Elena Provenzano
- Elias Campo
- Elisabet Barrera
- Elisabetta Sereni
- Elizabeth A Musgrove
- Elizabeth L Appelbaum
- Elizabeth L Christie
- Elli Papaemmanuil
- Ellrott Kyle
- Emilie Lalonde
- Eoghan Harrington
- Eric Chuah
- Eric Green
- Eric Lander
- Eric Minwei Liu
- Eric Z Ma
- Eric Z Ma
- Erik Garrison
- Erik Larsson
- Erik Mayer
- Erik N Bergstrom
- Erin Curley
- Ermin Hodzic
- Erwin G Van Meir
- Esa Pitkänen
- Esther Rheinbay
- Esther Rheinbay
- Eun Pyo Hong
- Eunjung Alice Lee
- Eva G Alvarez
- Eva Hellstrom-Lindberg
- Ewan Birney
- F Germán Rodríguez-González
- Fabien C Lamaze
- Fabien Calvo
- Fabio C P Navarro
- Faiyaz Notta
- Fan Yang
- Fan Zhang
- Faraz Hach
- Faraz Hach
- Faridah Mbabaali
- Fatima Al-Shahrour
- Federico Abascal
- Fei-Fei Liu
- Felicity Newell
- Fenglin Liu
- Fernanda Amary
- Ferran Muiños
- Florian Markowetz
- Fouad Yousif
- Francesc Muyas
- Francesco Favero
- Francisco M De La Vega
- Francisco Sanchez-Vega
- Fraser R Duthie
- Fred Sweep
- Freddie C Hamdy
- Fruzsina Molnár-Gábor
- Fumie Hosoda
- G Petur Nielsen
- G Steven Bova
- Gad Getz
- Gad Getz
- Gad Getz
- Gaetan MacGrogan
- Gaetano Finocchiaro
- Gary D Bader
- Gavin Ha
- Gavin W Wilson
- Genta Nagae
- Geoff Macintyre
- George B Hanna
- George L Mihaiescu
- Georgia Escaramis
- Georgina V Long
- Gerd Nettekoven
- German M Demidov
- German Ott
- Gerrit K Hooijer
- Gerstein Mark B
- Gert G Van den Eynden
- Getz Gad
- Ghislaine Scelo
- Giada Bonizzato
- Giampaolo Tortora
- Gilles Romieu
- Gilles Thomas
- Giovanni Marchegiani
- Gisela Mir Arnau
- Giuseppe Malleo
- Gloria M Petersen
- Gordon B Mills
- Gordon B Mills
- Gordon Saksena
- Gordon Saksena
- Gordon Saksena
- Grace Tiao
- Grace Tiao
- Graham J Mann
- Grant Sanders
- Gu Kong
- Guanming Wu
- Guido Reifenberger
- Guido Sauter
- Guillaume Bourque
- Gulietta M Pupo
- Gun Ho Jang
- Gunes Gundem
- Gunnar Rätsch
- Gurnit Atwal
- Hailei Zhang
- Haiyan Irene Li
- Han Liang
- Hana Susak
- Hans Binder
- Hans Lehrach
- Hans-Jörg Warnatz
- Hardeep K Nahal-Bose
- Hark Kyun Kim
- HarshaVardhan Doddapaneni
- Hartmut Juhl
- Harvey Pass
- Hayley C Whitaker
- Hayley J Luxton
- Hazel Burke
- Heather K Schmidt
- Heather Thorne
- Hee Jin Lee
- Heidi J Sofia
- Heidi Sofia
- Helen Davies
- Helena Kilpinen
- Helene Kretzmer
- Heng Xiong
- Henk G Stunnenberg
- Henrik Hornshøj
- Henry Lee-Six
- Hideki Ohdan
- Hidenori Ojima
- Hidewaki Nakagawa
- Hikmat Al-Ahmadie
- Hilda A Pickett
- Hirofumi Rokutan
- Hirokazu Taniguchi
- Hiroki Yamaue
- Hiroko Tanaka
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- Vincenzo Corbo
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- W Kimryn Rathmell
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- Wan Choi
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- Wang Liang-Bo
- Weerasinghe Amila
- Wei Jiao
- Wendl Michael C
- Wenyi Wang
- Wenyi Wang
- Wenyi Wang
- Wheeler David A
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- Xiaobo Li
- Xiaoping Su
- Xiaotong Li
- Xiaotong Yao
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- Xingmin Liu
- Xinyue Li
- Xiuqing Zhang
- Xiuqing Zheng
- Xose S Puente
- Xuan Le
- Xuanping Zhang
- Xuemei Luo
- Xueqing Zou
- Yan Shi
- Yan Zhang
- Yang Wu
- Yang Yang
- Yann Joly
- Yanxun Xu
- Yao He
- Yasin Senbabaoglu
- Yassen Assenov
- Yasser Riazalhosseini
- Yasuhito Arai
- Yasushi Rino
- Yasushi Totoki
- Yeng Ang
- Yi Huang
- Yi Huang
- Yifei Men
- Yiling Lu
- Yilong Li
- Yingyan Yu
- Yiwen Chen
- Yogesh Kumar
- Yogesh Kumar
- Yoke-Eng Chiew
- Yong Hou
- Yong Zhou
- Yong-Jie Lu
- Yongzhan Nie
- Yosef E Maruvka
- Yosef E Maruvka
- Yoshiiku Kawakami
- Young Seok Ju
- Youngchoon Woo
- Youngil Koh
- Youngwook Kim
- Youyong Lu
- Yu Fan
- Yu Fan
- Yu Fan
- Yu-Jia Shiah
- Yuan Ji
- Yuan Yuan
- Yuichi Shiraishi
- Yulia Newton
- Yulia Rubanova
- Yumeng Wang
- Yupeng Cun
- Yussanne Ma
- Zachary Heins
- Zechen Chong
- Zechen Chong
- Zemin Zhang
- Zhaohong Chen
- Zhenggang Wu
- Zhenggang Wu
- Zhining Wang
- Zhongming Zhao
- Ziao Lin
- Zsofia Kote-Jarai
- Ólafur Andri Stefánsson
- Øystein Garred
- Publication venue
- Nature Communications
- Publication date
- 01/01/2020
- Field of study
Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts
Sex differences in oncogenic mutational processes
- Author
- A Gordon Robertson
- Abdullah Kahraman
- Abel Gonzalez-Perez
- Adam A Margolin
- Adam Abeshouse
- Adam Grundhoff
- Adam J Struck
- Adam J Wright
- Adam Lambert
- Adam Margolin
- Adam P Butler
- Adel El-Naggar
- Adnan M Nagrial
- Adrian Ally
- Adrian Baez-Ortega
- Adrian Thorogood
- Adriana Salcedo
- Adrienne M Flanagan
- Ake Borg
- Akihiro Fujimoto
- Akihiro Suzuki
- Akinyemi I Ojesina
- Alain Viari
- Alan J Robertson
- Alan P Hoyle
- Alan Thompson
- Alasdair Stenhouse
- Alastair M Thompson
- Aldo Scarpa
- Alessandro Pastore
- Alex Buchanan
- Alexander Claviez
- Alexander J Lazar
- Alexander J Lazar
- Alexander Martinez-Fundichely
- Alfonso Muñoz
- Alfonso Valencia
- Aliaksei Z Holik
- Alice Meng
- Alicia L Bruzos
- Allison P Heath
- Alvin Wei Tian Ng
- Alvis Brazma
- Amaro Taylor-Weiner
- Amber L Johns
- Amit G Deshwar
- Ana Dueso-Barroso
- Ana Mijalkovic Mijalkovic-Lazic
- Ana Milovanovic
- Andre Kahles
- Andrea Haake
- Andrea Holbrook
- Andrea L Richardson
- Andrea Mafficini
- Andrea Ruzzenente
- Andreas Behren
- Andreas Rosenwald
- Andreia V Pinho
- Andrew Berchuck
- Andrew D Cherniack
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- Shinichi Mizuno
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- Shona MacRae
- Shriram G Bhosle
- Shuai Ding
- Shumpei Ishikawa
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- Subhajit Sengupta
- Sue Merson
- Suet-Feung Chin
- Sultan T Al-Sedairy
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- Tian Xia
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- Timothy J Underwood
- Tina Wong
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- Victor Reuter
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- Vincent J Gnanapragasam
- Vincent Khoo
- Vincenzo Corbo
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- Wan Choi
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- Wei Jiao
- Wei Jiao
- Wenyi Wang
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- William C Faquin
- William C Faquin
- William Friedman
- William Howat
- William Meyerson
- Willie Yu
- Winghing Wong
- Wojciech Bazant
- Wolfgang Huber
- Wolfram Klapper
- Xavier Estivill
- Xavier Pivot
- Xiao Xiao
- Xiaobo Li
- Xiaoping Su
- Xiaotong Li
- Xiaotong Yao
- Xing Hua
- Xingmin Liu
- Xinyue Li
- Xiuqing Zhang
- Xiuqing Zheng
- Xose S Puente
- Xuan Le
- Xuanping Zhang
- Xuemei Luo
- Xueqing Zou
- Yan Shi
- Yan Zhang
- Yang Wu
- Yang Yang
- Yann Joly
- Yanxun Xu
- Yao He
- Yasin Senbabaoglu
- Yassen Assenov
- Yasser Riazalhosseini
- Yasuhito Arai
- Yasushi Rino
- Yasushi Totoki
- Yeng Ang
- Yi Huang
- Yiling Lu
- Yilong Li
- Yingyan Yu
- Yiwen Chen
- Yogesh Kumar
- Yoke-Eng Chiew
- Yong Hou
- Yong Zhou
- Yong-Jie Lu
- Yongzhan Nie
- Yosef E Maruvka
- Yoshiiku Kawakami
- Young Seok Ju
- Youngchoon Woo
- Youngil Koh
- Youngwook Kim
- Yousif Fouad
- Youyong Lu
- Yu Fan
- Yu-Jia Shiah
- Yuan Ji
- Yuan Yuan
- Yuichi Shiraishi
- Yulia Newton
- Yulia Rubanova
- Yumeng Wang
- Yupeng Cun
- Yussanne Ma
- Zachary Heins
- Zechen Chong
- Zemin Zhang
- Zhaohong Chen
- Zhenggang Wu
- Zhining Wang
- Zhongming Zhao
- Ziao Lin
- Zsofia Kote-Jarai
- Ólafur Andri Stefánsson
- Øystein Garred
- Publication venue
- Publication date
- 01/01/2020
- Field of study
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe
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Sex differences in oncogenic mutational processes
- Author
- Aaltonen Lauri A.
- Abascal Federico
- Abeshouse Adam
- Aburatani Hiroyuki
- Adams David J.
- Agrawal Nishant
- Ahn Keun Soo
- Ahn Sung-Min
- Aikata Hiroshi
- Akbani Rehan
- Akdemir Kadir C.
- Al-Ahmadie Hikmat
- Al-Sedairy Sultan T.
- Al-Shahrour Fatima
- Alawi Malik
- Albert Monique
- Aldape Kenneth
- Alexandrov Ludmil B.
- Ally Adrian
- Alsop Kathryn
- Alvarez Eva G.
- Amary Fernanda
- Amin Samirkumar B.
- Aminou Brice
- Ammerpohl Ole
- Anderson Matthew J.
- Ang Yeng
- Antonello Davide
- Anur Pavana
- Aparicio Samuel
- Appelbaum Elizabeth L.
- Arai Yasuhito
- Aretz Axel
- Arihiro Koji
- Ariizumi Shun-ichi
- Armenia Joshua
- Arnau Gisela Mir
- Arnould Laurent
- Asa Sylvia
- Assenov Yassen
- Atwal Gurnit
- Aukema Sietse
- Auman J. Todd
- Aure Miriam R.
- Awadalla Philip
- Aymerich Marta
- Bader Gary D.
- Baez-Ortega Adrian
- Bailey Matthew H.
- Bailey Peter J.
- Balasundaram Miruna
- Balu Saianand
- Bandopadhayay Pratiti
- Banks Rosamonde E.
- Barbi Stefano
- Barbour Andrew P.
- Barenboim Jonathan
- Barnholtz-Sloan Jill
- Barr Hugh
- Barrera Elisabet
- Bartlett John
- Bartolome Javier
- Bassi Claudio
- Bathe Oliver F.
- Baumhoer Daniel
- Bavi Prashant
- Baylin Stephen B.
- Bazant Wojciech
- Beardsmore Duncan
- Beck Timothy A.
- Behjati Sam
- Behren Andreas
- Bell Cindy
- Beltran Sergi
- Benz Christopher
- Berchuck Andrew
- Bergmann Anke K.
- Bergstrom Erik N.
- Berman Benjamin P.
- Berney Daniel M.
- Bernhart Stephan H.
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- Hoyle Alan P.
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- Huang Mi Ni
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- Wu Guanming
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- Xi Liu
- Xia Tian
- Xiang Qian
- Xiao Xiao
- Xing Rui
- Xiong Heng
- Xu Qinying
- Xu Yanxun
- Xue Hong
- Yachida Shinichi
- Yakneen Sergei
- Yamaguchi Rui
- Yamaguchi Takafumi N.
- Yamamoto Masakazu
- Yamamoto Shogo
- Yamaue Hiroki
- Yang Fan
- Yang Huanming
- Yang Jean Y.
- Yang Liming
- Yang Lixing
- Yang Shanlin
- Yang Tsun-Po
- Yang Yang
- Yao Xiaotong
- Yaspo Marie-Laure
- Yates Lucy
- Yau Christina
- Ye Chen
- Ye Kai
- Yellapantula Venkata D.
- Yoon Christopher J.
- Yoon Sung-Soo
- Yousif Fouad
- Yu Jun
- Yu Kaixian
- Yu Willie
- Yu Yingyan
- Yuan Ke
- Yuan Yuan
- Yuen Denis
- Yugawa Takashi
- Yung Christina K.
- Zaikova Olga
- Zamora Jorge
- Zapatka Marc
- Zenklusen Jean C.
- Zenz Thorsten
- Zeps Nikolajs
- Zhang Cheng-Zhong
- Zhang Fan
- Zhang Hailei
- Zhang Hongwei
- Zhang Hongxin
- Zhang Jiashan
- Zhang Jing
- Zhang Junjun
- Zhang Xiuqing
- Zhang Xuanping
- Zhang Yan
- Zhang Zemin
- Zhao Zhongming
- Zheng Liangtao
- Zheng Xiuqing
- Zhou Wanding
- Zhou Yong
- Zhu Bin
- Zhu Hongtu
- Zhu Jingchun
- Zhu Shida
- Zou Lihua
- Zou Xueqing
- Publication venue
- Nature Communications
- Publication date
- 28/08/2020
- Field of study
Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- Aaltonen Lauri A.
- Abascal Federico
- Abeshouse Adam
- Aburatani Hiroyuki
- Adams David J.
- Agrawal Nishant
- Ahn Keun Soo
- Ahn Sung-Min
- Aikata Hiroshi
- Akbani Rehan
- Akdemir Kadir C.
- Al-Ahmadie Hikmat
- Al-Sedairy Sultan T.
- Al-Shahrour Fatima
- Alawi Malik
- Albert Monique
- Aldape Kenneth
- Alexandrov Ludmil B.
- Ally Adrian
- Alsop Kathryn
- Alvarez Eva G.
- Amary Fernanda
- Amin Samirkumar B.
- Aminou Brice
- Ammerpohl Ole
- Anderson Matthew J.
- Ang Yeng
- Antonello Davide
- Anur Pavana
- Aparicio Samuel
- Appelbaum Elizabeth L.
- Arai Yasuhito
- Aretz Axel
- Arihiro Koji
- Ariizumi Shun-ichi
- Armenia Joshua
- Arnau Gisela Mir
- Arnould Laurent
- Asa Sylvia
- Assenov Yassen
- Atwal Gurnit
- Aukema Sietse
- Auman J. Todd
- Aure Miriam R.
- Awadalla Philip
- Aymerich Marta
- Bader Gary D.
- Baez-Ortega Adrian
- Bailey Matthew H.
- Bailey Peter J.
- Balasundaram Miruna
- Balu Saianand
- Bandopadhayay Pratiti
- Banks Rosamonde E.
- Barbi Stefano
- Barbour Andrew P.
- Barenboim Jonathan
- Barnholtz-Sloan Jill
- Barr Hugh
- Barrera Elisabet
- Bartlett John
- Bartolome Javier
- Bassi Claudio
- Bathe Oliver F.
- Baumhoer Daniel
- Bavi Prashant
- Baylin Stephen B.
- Bazant Wojciech
- Beardsmore Duncan
- Beck Timothy A.
- Behjati Sam
- Behren Andreas
- Bell Cindy
- Beltran Sergi
- Benz Christopher
- Berchuck Andrew
- Bergmann Anke K.
- Bergstrom Erik N.
- Berman Benjamin P.
- Berney Daniel M.
- Bernhart Stephan H.
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- Gao Jianjiong
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- George Joshy
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- Yachida Shinichi
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- Yamaguchi Rui
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- Yao Xiaotong
- Yaspo Marie-Laure
- Yates Lucy
- Yau Christina
- Ye Chen
- Ye Kai
- Yellapantula Venkata D.
- Yoon Christopher J.
- Yoon Sung-Soo
- Yousif Fouad
- Yu Jun
- Yu Kaixian
- Yu Willie
- Yu Yingyan
- Yuan Ke
- Yuan Yuan
- Yuen Denis
- Yugawa Takashi
- Yung Christina K.
- Zaikova Olga
- Zamora Jorge
- Zapatka Marc
- Zenklusen Jean C.
- Zenz Thorsten
- Zeps Nikolajs
- Zhang Cheng-Zhong
- Zhang Fan
- Zhang Hailei
- Zhang Hongwei
- Zhang Hongxin
- Zhang Jiashan
- Zhang Jing
- Zhang Junjun
- Zhang Xiuqing
- Zhang Xuanping
- Zhang Yan
- Zhang Zemin
- Zhao Zhongming
- Zheng Liangtao
- Zheng Xiuqing
- Zhou Wanding
- Zhou Yong
- Zhu Hongtu
- Zhu Jingchun
- Zhu Shida
- Zou Lihua
- Zou Xueqing
- Publication venue
- Nature Communications
- Publication date
- 21/09/2020
- Field of study
Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- Author
- A Gordon Robertson
- Abdullah Kahraman
- Abel Gonzalez-Perez
- Adam A Margolin
- Adam Abeshouse
- Adam Grundhoff
- Adam J Struck
- Adam J Struck
- Adam J Wright
- Adam Lambert
- Adam P Butler
- Adam P Butler
- Adel El-Naggar
- Adnan M Nagrial
- Adrian Ally
- Adrian Baez-Ortega
- Adrian Thorogood
- Adriana Salcedo
- Adrienne M Flanagan
- Ake Borg
- Akihiro Fujimoto
- Akihiro Suzuki
- Akinyemi I Ojesina
- Alain Viari
- Alan J Robertson
- Alan P Hoyle
- Alan Thompson
- Alasdair Stenhouse
- Alastair M Thompson
- Aldo Scarpa
- Alessandro Pastore
- Alex Buchanan
- Alex Buchanan
- Alexander Claviez
- Alexander J Lazar
- Alexander Martinez-Fundichely
- Alfonso Muñoz
- Alfonso Valencia
- Aliaksei Z Holik
- Alice Meng
- Alicia L Bruzos
- Allison Creason
- Allison P Heath
- Alvin Wei Tian Ng
- Alvis Brazma
- Amaro Taylor-Weiner
- Amber L Johns
- Amie Radenbaugh
- Amit G Deshwar
- Ana Dueso-Barroso
- Ana Mijalkovic Mijalkovic-Lazic
- Ana Milovanovic
- Ana Milovanovic
- Andre Kahles
- Andrea Haake
- Andrea Holbrook
- Andrea L Richardson
- Andrea Mafficini
- Andrea Ruzzenente
- Andreas Behren
- Andreas Rosenwald
- Andreia V Pinho
- Andrew Berchuck
- Andrew D Cherniack
- Andrew J Dunford
- Andrew J Mungall
- Andrew J Spillane
- Andrew Menzies
- Andrew Menzies
- Andrew P Barbour
- Andrew Tutt
- Andrew V Biankin
- Andrey Korshunov
- Andrés Lanzós
- Andy Cafferkey
- Andy G Lynch
- Angela Chou
- Angela N Brooks
- Angela Tam
- Angelica Ochoa
- Angelika N Christ
- Angelo P Dei Tos
- Anieta M Sieuwerts
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- Sangeetha Kalimuthu
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- Santiago Gonzalez
- Santiago Gonzalez
- Sara Cingarlini
- Sara Sadeghi
- Sarah Minner
- Sarah O'Meara
- Sarah P Thayer
- Sarah Pinder
- Sarah Thomas
- Sarah-Jane Schramm
- Satoru Miyano
- Satoshi Hirano
- Savitri Krishnamurthy
- Scott Frazer
- Scott Wood
- Se Jin Jang
- Sean Cleary
- Sean M Grimmond
- Sebastian M Waszak
- Sebastian M Waszak
- Seiya Imoto
- Seong Gu Heo
- Serap Erkek
- Serena Nik-Zainal
- Serge Serge
- Sergei Yakneen
- Sergei Yakneen
- Sergi Beltran
- Sergio Pulido-Tamayo
- Seung Jun Shin
- Seung-Hyup Jeon
- Shadrielle M G Espiritu
- Shadrielle M G Espiritu
- Shailja Gupta
- Shankar Vembu
- Shanlin Yang
- Shantao Li
- Shaoke Lou
- Shaolong Cao
- Shaowu Meng
- Sharmila Sothi
- Shaun R Preston
- Sheila M Reynolds
- Sheila M Reynolds
- Sheng-Ben Liang
- Shengjie Gao
- Shengjie Gao
- Shida Zhu
- Shimin Shuai
- Shinichi Mizuno
- Shinichi Yachida
- Shinya Hayami
- Shogo Yamamoto
- Shona MacRae
- Shriram G Bhosle
- Shuai Ding
- Shumpei Ishikawa
- Shun-Ichi Ariizumi
- Shuto Hayashi
- Sian Fereday
- Siegfried Haas
- Sietse Aukema
- Siliang Li
- Simon C Heath
- Simon L Parsons
- Simon Mayes
- Simon Tavaré
- Simpson Jared T
- Singer Ma
- Sinisa Ivkovic
- Sissel Juul
- Solomon I Shorser
- Sonia Grimaldi
- Sonia Puig
- Stacey B Gabriel
- Stefan C Dentro
- Stefan G Stark
- Stefan M Pfister
- Stefan Schreiber
- Stefania Tommasi
- Stefano Barbi
- Stefano Serra
- Stephan H Bernhart
- Stephan Ossowski
- Stephan Ossowski
- Stephan Stilgenbauer
- Stephan Wolf
- Stephanie Sungalee
- Stephen B Baylin
- Stephen H Kazakoff
- Stephen J Chanock
- Stephen J Hayes
- Stephen M Cordner
- Stephenie D Prokopec
- Steve Hawkins
- Steve Hoffmann
- Steven A Roberts
- Steven E Schumacher
- Steven Foltz
- Steven G Rozen
- Steven Gallinger
- Steven Hazell
- Steven J M Jones
- Steven J Newhouse
- Steven Van Laere
- Stian Knappskog
- Stuart Edmonds
- Stuart R Jefferys
- Su Pin Choo
- Subhajit Sengupta
- Sue Merson
- Suet-Feung Chin
- Sultan T Al-Sedairy
- Sung-Min Ahn
- Sung-Soo Yoon
- Sunghoon Cho
- Sunil R Lakhani
- Suresh Ramalingam
- Susan Bullman
- Susanna L Cooke
- Sushant Kumar
- Sushant Kumar
- Suyash S Shringarpure
- Syed Haider
- Sylvia Asa
- Søren Brunak
- Takafumi N Yamaguchi
- Takafumi N Yamaguchi
- Takanori Hasegawa
- Takashi Yugawa
- Takashi Yugawa
- Takuji Okusaka
- Tal Shmaya
- Tannistha Nandi
- Taobo Hu
- Taobo Hu
- Tapio Visakorpi
- Tara J Skelly
- Tari A King
- Tatsuhiko Tsunoda
- Tatsuhiro Shibata
- Ted R Hupp
- Tetsuo Ushiku
- Theodorus Van der Kwast
- Thomas E Carey
- Thomas J Hudson
- Thomas J Matthew
- Thomas J Mitchell
- Thorsten Schlomm
- Thorsten Zenz
- Tian Xia
- Tim Dudderidge
- Tim Ley
- Timothy A Beck
- Timothy Defreitas
- Timothy J C Bruxner
- Timothy J Underwood
- Tina Wong
- Tirso Pons
- Tobias Madsen
- Tobias Rausch
- Todd A Johnson
- Todd D Pihl
- Tom Bodenheimer
- Tom Mikkelsen
- Tom Roques
- Tomas J Tanskanen
- Tomas Marques-Bonet
- Tomoko Urushidate
- Torill Sauer
- Toru Nakamura
- Treasa A McPherson
- Troy Shelton
- Tsun-Po Yang
- Ultan McDermott
- Umadevi Veluvolu
- Umut H Toprak
- Valerie Jakrot
- Varsha Tembe
- Vasilisa A Rudneva
- Venkata D Yellapantula
- Venkata D Yellapantula
- Vera B Kaiser
- Veronica Y Sabelnykova
- Victor Reuter
- Vikram Deshpande
- Viktoriya Korchina
- Ville Mustonen
- Vinayak Bhandari
- Vincent Ferretti
- Vincent Huang
- Vincent Huang
- Vincent J Gnanapragasam
- Vincent Khoo
- Vincenzo Corbo
- Vishal S Chandan
- Volker Hovestadt
- W Kimryn Rathmell
- W M Linehan
- Walker Hale
- Wan Choi
- Wanding Zhou
- Wang Liang-Bo
- Weerasinghe Amila
- Wei Jiao
- Wendl Michael C
- Wenyi Wang
- Wenyi Wang
- Wenyi Wang
- Wheeler David A
- William B Isaacs
- William C Faquin
- William Friedman
- William Howat
- William U Meyerson
- Willie Yu
- Winghing Wong
- Wojciech Bazant
- Wolfgang Huber
- Wolfram Klapper
- Xavier Estivill
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- Xiao Xiao
- Xiaobo Li
- Xiaoping Su
- Xiaotong Li
- Xiaotong Yao
- Xing Hua
- Xingmin Liu
- Xinyue Li
- Xiuqing Zhang
- Xiuqing Zheng
- Xose S Puente
- Xuan Le
- Xuanping Zhang
- Xuemei Luo
- Xueqing Zou
- Yan Shi
- Yan Zhang
- Yang Wu
- Yang Yang
- Yann Joly
- Yanxun Xu
- Yao He
- Yasin Senbabaoglu
- Yassen Assenov
- Yasser Riazalhosseini
- Yasuhito Arai
- Yasushi Rino
- Yasushi Totoki
- Yeng Ang
- Yi Huang
- Yi Huang
- Yifei Men
- Yiling Lu
- Yilong Li
- Yingyan Yu
- Yiwen Chen
- Yogesh Kumar
- Yogesh Kumar
- Yoke-Eng Chiew
- Yong Hou
- Yong Zhou
- Yong-Jie Lu
- Yongzhan Nie
- Yosef E Maruvka
- Yosef E Maruvka
- Yoshiiku Kawakami
- Young Seok Ju
- Youngchoon Woo
- Youngil Koh
- Youngwook Kim
- Youyong Lu
- Yu Fan
- Yu Fan
- Yu Fan
- Yu-Jia Shiah
- Yuan Ji
- Yuan Yuan
- Yuichi Shiraishi
- Yulia Newton
- Yulia Rubanova
- Yumeng Wang
- Yupeng Cun
- Yussanne Ma
- Zachary Heins
- Zechen Chong
- Zechen Chong
- Zemin Zhang
- Zhaohong Chen
- Zhenggang Wu
- Zhenggang Wu
- Zhining Wang
- Zhongming Zhao
- Ziao Lin
- Zsofia Kote-Jarai
- Ólafur Andri Stefánsson
- Øystein Garred
- Publication venue
- Publication date
- 01/01/2020
- Field of study
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe