Literature DB >> 33655273

A catalog of associations between rare coding variants and COVID-19 outcomes.

J A Kosmicki, J E Horowitz, N Banerjee, R Lanche, A Marcketta, E Maxwell, X Bai, D Sun, J D Backman, D Sharma, H M Kang, C O'Dushlaine, A Yadav, A J Mansfield, A H Li, K Watanabe, L Gurski, S E McCarthy, A E Locke, S Khalid, S O'Keeffe, J Mbatchou, O Chazara, Y Huang, E Kvikstad, A O'Neill, P Nioi, M M Parker, S Petrovski, H Runz, J D Szustakowski, Q Wang, E Wong, A Cordova-Palomera, E N Smith, S Szalma, X Zheng, S Esmaeeli, J W Davis, Y-P Lai, X Chen, A E Justice, J B Leader, T Mirshahi, D J Carey, A Verma, G Sirugo, M D Ritchie, D J Rader, G Povysil, D B Goldstein, K Kiryluk, E Pairo-Castineira, K Rawlik, D Pasko, S Walker, A Meynert, A Kousathanas, L Moutsianas, A Tenesa, M Caulfield, R Scott, J F Wilson, J K Baillie, G Butler-Laporte, T Nakanishi, M Lathrop, J B Richards, M Jones, S Balasubramanian, W Salerno, A R Shuldiner, J Marchini, J D Overton, L Habegger, M N Cantor, J G Reid, A Baras, G R Abecasis, M A Ferreira.   

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com .

Entities:  

Year:  2021        PMID: 33655273      PMCID: PMC7924298          DOI: 10.1101/2020.10.28.20221804

Source DB:  PubMed          Journal:  medRxiv


  41 in total

1.  Million Veteran Program: A mega-biobank to study genetic influences on health and disease.

Authors:  John Michael Gaziano; John Concato; Mary Brophy; Louis Fiore; Saiju Pyarajan; James Breeling; Stacey Whitbourne; Jennifer Deen; Colleen Shannon; Donald Humphries; Peter Guarino; Mihaela Aslan; Daniel Anderson; Rene LaFleur; Timothy Hammond; Kendra Schaa; Jennifer Moser; Grant Huang; Sumitra Muralidhar; Ronald Przygodzki; Timothy J O'Leary
Journal:  J Clin Epidemiol       Date:  2015-10-09       Impact factor: 6.437

2.  SIFT missense predictions for genomes.

Authors:  Robert Vaser; Swarnaseetha Adusumalli; Sim Ngak Leng; Mile Sikic; Pauline C Ng
Journal:  Nat Protoc       Date:  2015-12-03       Impact factor: 13.491

3.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Authors:  Kim D Pruitt; Jennifer Harrow; Rachel A Harte; Craig Wallin; Mark Diekhans; Donna R Maglott; Steve Searle; Catherine M Farrell; Jane E Loveland; Barbara J Ruef; Elizabeth Hart; Marie-Marthe Suner; Melissa J Landrum; Bronwen Aken; Sarah Ayling; Robert Baertsch; Julio Fernandez-Banet; Joshua L Cherry; Val Curwen; Michael Dicuccio; Manolis Kellis; Jennifer Lee; Michael F Lin; Michael Schuster; Andrew Shkeda; Clara Amid; Garth Brown; Oksana Dukhanina; Adam Frankish; Jennifer Hart; Bonnie L Maidak; Jonathan Mudge; Michael R Murphy; Terence Murphy; Jeena Rajan; Bhanu Rajput; Lillian D Riddick; Catherine Snow; Charles Steward; David Webb; Janet A Weber; Laurens Wilming; Wenyu Wu; Ewan Birney; David Haussler; Tim Hubbard; James Ostell; Richard Durbin; David Lipman
Journal:  Genome Res       Date:  2009-06-04       Impact factor: 9.043

4.  Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.

Authors:  Goo Jun; Matthew Flickinger; Kurt N Hetrick; Jane M Romm; Kimberly F Doheny; Gonçalo R Abecasis; Michael Boehnke; Hyun Min Kang
Journal:  Am J Hum Genet       Date:  2012-10-25       Impact factor: 11.025

5.  Presence of Genetic Variants Among Young Men With Severe COVID-19.

Authors:  Caspar I van der Made; Annet Simons; Janneke Schuurs-Hoeijmakers; Guus van den Heuvel; Tuomo Mantere; Simone Kersten; Rosanne C van Deuren; Marloes Steehouwer; Simon V van Reijmersdal; Martin Jaeger; Tom Hofste; Galuh Astuti; Jordi Corominas Galbany; Vyne van der Schoot; Hans van der Hoeven; Wanda Hagmolen Of Ten Have; Eva Klijn; Catrien van den Meer; Jeroen Fiddelaers; Quirijn de Mast; Chantal P Bleeker-Rovers; Leo A B Joosten; Helger G Yntema; Christian Gilissen; Marcel Nelen; Jos W M van der Meer; Han G Brunner; Mihai G Netea; Frank L van de Veerdonk; Alexander Hoischen
Journal:  JAMA       Date:  2020-08-18       Impact factor: 56.272

6.  From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.

Authors:  Geraldine A Van der Auwera; Mauricio O Carneiro; Christopher Hartl; Ryan Poplin; Guillermo Del Angel; Ami Levy-Moonshine; Tadeusz Jordan; Khalid Shakir; David Roazen; Joel Thibault; Eric Banks; Kiran V Garimella; David Altshuler; Stacey Gabriel; Mark A DePristo
Journal:  Curr Protoc Bioinformatics       Date:  2013

7.  BinomiRare: A robust test of the association of a rare variant with a disease for pooled analysis and meta-analysis, with application to the HCHS/SOL.

Authors:  Tamar Sofer
Journal:  Genet Epidemiol       Date:  2017-04-10       Impact factor: 2.135

8.  Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.

Authors:  Israel S Fernández; Xiao-Chen Bai; Garib Murshudov; Sjors H W Scheres; V Ramakrishnan
Journal:  Cell       Date:  2014-05-01       Impact factor: 41.582

9.  Genomewide Association Study of Severe Covid-19 with Respiratory Failure.

Authors:  David Ellinghaus; Frauke Degenhardt; Luis Bujanda; Maria Buti; Agustín Albillos; Pietro Invernizzi; Javier Fernández; Daniele Prati; Guido Baselli; Rosanna Asselta; Marit M Grimsrud; Chiara Milani; Fátima Aziz; Jan Kässens; Sandra May; Mareike Wendorff; Lars Wienbrandt; Florian Uellendahl-Werth; Tenghao Zheng; Xiaoli Yi; Raúl de Pablo; Adolfo G Chercoles; Adriana Palom; Alba-Estela Garcia-Fernandez; Francisco Rodriguez-Frias; Alberto Zanella; Alessandra Bandera; Alessandro Protti; Alessio Aghemo; Ana Lleo; Andrea Biondi; Andrea Caballero-Garralda; Andrea Gori; Anja Tanck; Anna Carreras Nolla; Anna Latiano; Anna Ludovica Fracanzani; Anna Peschuck; Antonio Julià; Antonio Pesenti; Antonio Voza; David Jiménez; Beatriz Mateos; Beatriz Nafria Jimenez; Carmen Quereda; Cinzia Paccapelo; Christoph Gassner; Claudio Angelini; Cristina Cea; Aurora Solier; David Pestaña; Eduardo Muñiz-Diaz; Elena Sandoval; Elvezia M Paraboschi; Enrique Navas; Félix García Sánchez; Ferruccio Ceriotti; Filippo Martinelli-Boneschi; Flora Peyvandi; Francesco Blasi; Luis Téllez; Albert Blanco-Grau; Georg Hemmrich-Stanisak; Giacomo Grasselli; Giorgio Costantino; Giulia Cardamone; Giuseppe Foti; Serena Aneli; Hayato Kurihara; Hesham ElAbd; Ilaria My; Iván Galván-Femenia; Javier Martín; Jeanette Erdmann; Jose Ferrusquía-Acosta; Koldo Garcia-Etxebarria; Laura Izquierdo-Sanchez; Laura R Bettini; Lauro Sumoy; Leonardo Terranova; Leticia Moreira; Luigi Santoro; Luigia Scudeller; Francisco Mesonero; Luisa Roade; Malte C Rühlemann; Marco Schaefer; Maria Carrabba; Mar Riveiro-Barciela; Maria E Figuera Basso; Maria G Valsecchi; María Hernandez-Tejero; Marialbert Acosta-Herrera; Mariella D'Angiò; Marina Baldini; Marina Cazzaniga; Martin Schulzky; Maurizio Cecconi; Michael Wittig; Michele Ciccarelli; Miguel Rodríguez-Gandía; Monica Bocciolone; Monica Miozzo; Nicola Montano; Nicole Braun; Nicoletta Sacchi; Nilda Martínez; Onur Özer; Orazio Palmieri; Paola Faverio; Paoletta Preatoni; Paolo Bonfanti; Paolo Omodei; Paolo Tentorio; Pedro Castro; Pedro M Rodrigues; Aaron Blandino Ortiz; Rafael de Cid; Ricard Ferrer; Roberta Gualtierotti; Rosa Nieto; Siegfried Goerg; Salvatore Badalamenti; Sara Marsal; Giuseppe Matullo; Serena Pelusi; Simonas Juzenas; Stefano Aliberti; Valter Monzani; Victor Moreno; Tanja Wesse; Tobias L Lenz; Tomas Pumarola; Valeria Rimoldi; Silvano Bosari; Wolfgang Albrecht; Wolfgang Peter; Manuel Romero-Gómez; Mauro D'Amato; Stefano Duga; Jesus M Banales; Johannes R Hov; Trine Folseraas; Luca Valenti; Andre Franke; Tom H Karlsen
Journal:  N Engl J Med       Date:  2020-06-17       Impact factor: 91.245

10.  GenPipes: an open-source framework for distributed and scalable genomic analyses.

Authors:  Mathieu Bourgey; Rola Dali; Robert Eveleigh; Kuang Chung Chen; Louis Letourneau; Joel Fillon; Marc Michaud; Maxime Caron; Johanna Sandoval; Francois Lefebvre; Gary Leveque; Eloi Mercier; David Bujold; Pascale Marquis; Patrick Tran Van; David Anderson de Lima Morais; Julien Tremblay; Xiaojian Shao; Edouard Henrion; Emmanuel Gonzalez; Pierre-Olivier Quirion; Bryan Caron; Guillaume Bourque
Journal:  Gigascience       Date:  2019-06-01       Impact factor: 6.524

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  4 in total

1.  Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants.

Authors:  Diogo Pellegrina; Alexander T Bahcheli; Michal Krassowski; Jüri Reimand
Journal:  Mol Syst Biol       Date:  2022-05       Impact factor: 13.068

2.  COVID-19 in pediatrics: Genetic susceptibility.

Authors:  Joseph T Glessner; Xiao Chang; Frank Mentch; Huiqi Qu; Debra J Abrams; Alexandria Thomas; Patrick M A Sleiman; Hakon Hakonarson
Journal:  Front Genet       Date:  2022-08-16       Impact factor: 4.772

3.  Genetic map of regional sulcal morphology in the human brain from UK biobank data.

Authors:  Stephanie J Loomis; Fabrizio Pizzagalli; Benjamin B Sun; Natalia Shatokhina; Jodie N Painter; Christopher N Foley; Megan E Jensen; Donald G McLaren; Sai Spandana Chintapalli; Alyssa H Zhu; Daniel Dixon; Tasfiya Islam; Iyad Ba Gari; Heiko Runz; Sarah E Medland; Paul M Thompson; Neda Jahanshad; Christopher D Whelan
Journal:  Nat Commun       Date:  2022-10-14       Impact factor: 17.694

4.  Mapping the human genetic architecture of COVID-19.

Authors: 
Journal:  Nature       Date:  2021-07-08       Impact factor: 69.504

  4 in total

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