Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity
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Published:2021-12-10
Issue:1
Volume:141
Page:147-173
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ISSN:0340-6717
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Container-title:Human Genetics
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language:en
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Short-container-title:Hum Genet
Author:
Fallerini Chiara, Picchiotti Nicola, Baldassarri Margherita, Zguro Kristina, Daga Sergio, Fava Francesca, Benetti Elisa, Amitrano Sara, Bruttini Mirella, Palmieri Maria, Croci Susanna, Lista Mirjam, Beligni Giada, Valentino Floriana, Meloni Ilaria, Tanfoni Marco, Minnai Francesca, Colombo Francesca, Cabri Enrico, Fratelli Maddalena, Gabbi Chiara, Mantovani Stefania, Frullanti Elisa, Gori Marco, Crawley Francis P., Butler-Laporte Guillaume, Richards Brent, Zeberg Hugo, Lipcsey Miklos, Hultström Michael, Ludwig Kerstin U., Schulte Eva C., Pairo-Castineira Erola, Baillie John Kenneth, Schmidt Axel, Frithiof Robert, Furini Simone, Montagnani Francesca, Tumbarello Mario, Rancan Ilaria, Fabbiani Massimiliano, Rossetti Barbara, Bergantini Laura, D’Alessandro Miriana, Cameli Paolo, Bennett David, Anedda Federico, Marcantonio Simona, Scolletta Sabino, Franchi Federico, Mazzei Maria Antonietta, Guerrini Susanna, Conticini Edoardo, Cantarini Luca, Frediani Bruno, Tacconi Danilo, Raffaelli Chiara Spertilli, Feri Marco, Donati Alice, Scala Raffaele, Guidelli Luca, Spargi Genni, Corridi Marta, Nencioni Cesira, Croci Leonardo, Caldarelli Gian Piero, Spagnesi Maurizio, Romani Davide, Piacentini Paolo, Bandini Maria, Desanctis Elena, Cappelli Silvia, Canaccini Anna, Verzuri Agnese, Anemoli Valentina, Pisani Manola, Ognibene Agostino, Pancrazzi Alessandro, Lorubbio Maria, Vaghi Massimo, Monforte Antonella D.’Arminio, Miraglia Federica Gaia, Mondelli Mario U., Girardis Massimo, Venturelli Sophie, Busani Stefano, Cossarizza Andrea, Antinori Andrea, Vergori Alessandra, Emiliozzi Arianna, Rusconi Stefano, Siano Matteo, Gabrieli Arianna, Riva Agostino, Francisci Daniela, Schiaroli Elisabetta, Paciosi Francesco, Tommasi Andrea, Scotton Pier Giorgio, Andretta Francesca, Panese Sandro, Baratti Stefano, Scaggiante Renzo, Gatti Francesca, Parisi Saverio Giuseppe, Castelli Francesco, Quiros-Roldan Eugenia, Antoni Melania Degli, Zanella Isabella, Monica Matteo Della, Piscopo Carmelo, Capasso Mario, Russo Roberta, Andolfo Immacolata, Iolascon Achille, Fiorentino Giuseppe, Carella Massimo, Castori Marco, Aucella Filippo, Raggi Pamela, Perna Rita, Bassetti Matteo, Di Biagio Antonio, Sanguinetti Maurizio, Masucci Luca, Guarnaccia Alessandra, Valente Serafina, De Vivo Oreste, Doddato Gabriella, Tita Rossella, Giliberti Annarita, Mencarelli Maria Antonietta, Rizzo Caterina Lo, Pinto Anna Maria, Perticaroli Valentina, Ariani Francesca, Carriero Miriam Lucia, Di Sarno Laura, Alaverdian Diana, Bargagli Elena, Mandalà Marco, Giorli Alessia, Salerni Lorenzo, Zucchi Patrizia, Parravicini Pierpaolo, Menatti Elisabetta, Trotta Tullio, Giannattasio Ferdinando, Coiro Gabriella, Lena Fabio, Lacerenza Leonardo Gianluca, Coviello Domenico A., Mussini Cristina, Martinelli Enrico, Mancarella Sandro, Tavecchia Luisa, Belli Mary Ann, Crotti Lia, Parati Gianfranco, Sanarico Maurizio, Raimondi Francesco, Biscarini Filippo, Stella Alessandra, Rizzi Marco, Maggiolo Franco, Ripamonti Diego, Suardi Claudia, Bachetti Tiziana, La Rovere Maria Teresa, Sarzi-Braga Simona, Bussotti Maurizio, Capitani Katia, Dei Simona, Ravaglia Sabrina, Artuso Rosangela, Andreucci Elena, Gori Giulia, Pagliazzi Angelica, Fiorentini Erika, Perrella Antonio, Bianchi Francesco, Bergomi Paola, Catena Emanuele, Colombo Riccardo, Luchi Sauro, Morelli Giovanna, Petrocelli Paola, Iacopini Sarah, Modica Sara, Baroni Silvia, Segala Francesco Vladimiro, Menichetti Francesco, Falcone Marco, Tiseo Giusy, Barbieri Chiara, Matucci Tommaso, Grassi Davide, Ferri Claudio, Marinangeli Franco, Brancati Francesco, Vincenti Antonella, Borgo Valentina, Stefania Lombardi, Lenzi Mirco, Di Pietro Massimo Antonio, Vichi Francesca, Romanin Benedetta, Attala Letizia, Costa Cecilia, Gabbuti Andrea, Roberto Menè, Zuccon Umberto, Vietri Lucia, Ceri Stefano, Pinoli Pietro, Casprini Patrizia, Merla Giuseppe, Squeo Gabriella Maria, Maffezzoni Marcello, Bruno Raffaele, Vecchia Marco, Colaneri Marta, Ludovisi Serena, Marincevic-Zuniga Yanara, Nordlund Jessica, Luther Tomas, Larsson Anders, Gradin Katja Hanslin Anna, Galien Sarah, Anderberg Sara Bulow, Rosén Jacob, Rubertsson Sten, Zeberg Hugo, Frithiof Robert, Lipcsey Miklós, Hultström Michael, Horby Sara Clohisey Peter, Millar Johnny, Knight Julian, Montgomery Hugh, Maslove David, Ling Lowell, Nichol Alistair, Summers Charlotte, Walsh Tim, Hinds Charles, Semple Malcolm G., Openshaw Peter J. M., Shankar-Hari Manu, Ho Antonia, McAuley Danny, Ponting Chris, Rowan Kathy, Baillie J. Kenneth, Griffiths Fiona, Oosthuyzen Wilna, Meikle Jen, Finernan Paul, Furniss James, Mcmaster Ellie, Law Andy, Clohisey Sara, Baillie J. Kenneth, Paterson Trevor, Wackett Tony, Armstrong Ruth, Murphy Lee, Fawkes Angie, Clark Richard, Coutts Audrey, Donnelly Lorna, Gilchrist Tammy, Hafezi Katarzyna, Macgillivray Louise, Maclean Alan, McCafferty Sarah, Morrice Kirstie, Weaver Jane, Boz Ceilia, Golightly Ailsa, Ward Mari, Mal Hanning, Szoor-McElhinney Helen, Brown Adam, Hendry Ross, Stenhouse Andrew, Cullum Louise, Law Dawn, Law Sarah, Law Rachel, Fourman Max Head, Swets Maaike, Day Nicky, Taneski Filip, Duncan Esther, Zechner Marie, Parkinson Nicholas, Pairo-Castineira Erola, Clohisey Sara, Klaric Lucija, Bretherick Andrew D., Rawlik Konrad, Pasko Dorota, Walker Susan, Parkinson Nick, Fourman Max Head, Russell Clark D., Furniss James, Richmond Anne, Gountouna Elvina, Harrison David, Wang Bo, Wu Yang, Meynert Alison, Kousathanas Athanasios, Moutsianas Loukas, Yang Zhijian, Zhai Ranran, Zheng Chenqing, Grimes Graeme, Millar Jonathan, Shih Barbara, Zechner Marie, Yang Jian, Shen Xia, Ponting Chris P., Tenesa Albert, Rowan Kathy, Law Andrew, Vitart Veronique, Wilson James F., Baillie J. Kenneth, Collier D., Wood S., Zak A., Borra C., Matharu M., May P., Alldis Z., Mitchelmore O., Bowles R., Easthorpe A., Bibi F., Lancoma-Malcolm I., Gurasashvili J., Pheby J., Shiel J., Bolton M., Patel M., Taylor M., Zongo O., Ebano P., Harding P., Astin-Chamberlain R., Choudhury Y., Cox A., Kallon D., Burton M., Hall R., Blowes S., Prime Z., Biddle J., Prysyazhna O., Newman T., Tierney C., Kassam J., Shankar-Hari M., Ostermann M., Campos S., Bociek A., Lim R., Grau N., Jones T. O., Whitton C., Marotti M., Arbane G., Bonner S., Hugill K., Reid J., Welters I., Waugh V., Williams K., Shaw D., Roman J. Fernandez, Martinez M. Lopez, Johnson E., Waite A., Johnson B., Hamilton O., Mulla S., McPhail M., Smith J., Baillie J. 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Moreno, Haldeos A., Bakthavatsalam D., Vincent R., Elhassan M., Xavier K., Ganesan A., Purohit D., Abdelrazik M., Morgan J., Akeroyd L., Bano S., Warren D., Bromley M., Sellick K., Gurr L., Wilkinson B., Nagarajan V., Szedlak P., Cupitt J., Stoddard E., Benham L., Preston S., Slawson N., Bradshaw Z., brown J., Caswell M., SMelling , Bamford P., Faulkner M., Cawley K., Jeffrey H., London E., Sainsbury H., Nagra I., Nasir F., Dunmore Ce, Jones R., Abraheem A., Al-Moasseb M., Girach R., Brantwood C., Alexander P., Bradley-Potts J., Allen S., Felton T., Manna S., Farnell-Ward S., Leaver S., Queiroz J., Maccacari E., Dawson D., Delgado C. Castro, Saluzzio R. 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Brent, Butler-Laporte Guillaume, Kwasniewski Mirosław, Korotko Urszula, Chwialkowska Karolina, Niemira Magdalena, Jaroszewicz Jerzy, Sobala-Szczygiel Barbara, Puzanowska Beata, Parfieniuk-Kowerda Anna, Martonik Diana, Moniuszko-Malinowska Anna, Pancewicz Sławomir, Zarębska-Michaluk Dorota, Simon Krzysztof, Pazgan-Simon Monika, Mozer-Lisewska Iwona, Bura Maciej, Adamek Agnieszka, Pawłowska Krzysztof Tomasiewicz Małgorzata, Piekarska Anna, Berkan-Kawinska Aleksandra, Horban Andrzej, Kowalska Justyna, Podlasin Regina, Wasilewski Piotr, Azzadin Arsalin, Czuczwar Miroslaw, Czaban Slawomir, Olszewski Paweł, Bogocz Jacek, Ochab Magdalena, Kruk Anna, Uszok Sandra, Bielska Agnieszka, Szałkowska Anna, Raczkowska Justyna, Sokołowska Gabriela, Chorostowska-Wynimko Joanna, Jezela-Stanek Aleksandra, Roży Adriana, Lechowicz Urszula, Polowianiuk Urszula, Grubczak Kamil, Starosz Aleksandra, Eljaszewicz Andrzej, Izdebska Wiktoria, Krętowski Adam, Flisiak Robert, Alaamery Marcin Moniuszko, Malak Abedalthaga, Massadeh Salam, Fawzy Mohamed, AlBardis Hadeel, Aljawini Nora, Alsuwailm Moneera, Almalki Faisal, Mangul Serghei, Jung Junghyun, Mbarek Hamdi, Saad Chadi, Al-Sarraj Yaser, Al-Muftah Wadha, Badji Radja, Al Thani Asma, Ismail Said I., Mari Francesca, Renieri AlessandraORCID, Furini Simone, , ,
Abstract
AbstractThe combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management.
Funder
MIUR Bando Ricerca COVID-19 Toscana Italian Ministry of University and Research Center for Sepsis Control and Care Canadian Institutes of Health Research
Publisher
Springer Science and Business Media LLC
Subject
Genetics (clinical),Genetics
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