High-throughput DNA extraction and genotyping

We performed DNA extraction using a Chemagic 360 (PerkinElmer) with the use of the low-volume kit CMG-1491 and the buffy-coat kit CMG-714 (Chemagen), respectively. For genotyping, we used the Global Screening Array (GSA), version 2.0 (Illumina), which contains 712,189 variants before quality control. Details on genotyping and quality-control procedures are provided in the Supplementary Methods section in Supplementary Appendix 1. To maximize genetic coverage, we performed single-nucleotide polymorphism (SNP) imputation on genome build GRCh38 using the Michigan Imputation Server and 194,512 haplotypes generated by the Trans-Omics for Precision Medicine (TOPMed) program (freeze 5).¹⁶After the exclusion of samples during quality control (the majority of which were due to population outliers; see the Supplementary Methods section and Table S1B and S1C), the final case–control data sets comprised 835 patients and 1255 control participants from Italy and 775 patients and 950 control participants from Spain. A total of 8,965,091 SNPs were included in the Italian cohort and 9,140,716 SNPs in the Spanish cohort.

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Ellinghaus D., Degenhardt F., Bujanda L., Buti M., Albillos A., Invernizzi P., Fernández J., Prati D., Baselli G., Asselta R., Grimsrud M.M., Milani C., Aziz F., Kässens J., May S., Wendorff M., Wienbrandt L., Uellendahl-Werth F., Zheng T., Yi X., de Pablo R., Chercoles A.G., Palom A., Garcia-Fernandez A.E., Rodriguez-Frias F., Zanella A., Bandera A., Protti A., Aghemo A., Lleo A., Biondi A., Caballero-Garralda A., Gori A., Tanck A., Carreras Nolla A., Latiano A., Fracanzani A.L., Peschuck A., Julià A., Pesenti A., Voza A., Jiménez D., Mateos B., Nafria Jimenez B., Quereda C., Paccapelo C., Gassner C., Angelini C., Cea C., Solier A., Pestaña D., Muñiz-Diaz E., Sandoval E., Paraboschi E.M., Navas E., García Sánchez F., Ceriotti F., Martinelli-Boneschi F., Peyvandi F., Blasi F., Téllez L., Blanco-Grau A., Hemmrich-Stanisak G., Grasselli G., Costantino G., Cardamone G., Foti G., Aneli S., Kurihara H., ElAbd H., My I., Galván-Femenia I., Martín J., Erdmann J., Ferrusquía-Acosta J., Garcia-Etxebarria K., Izquierdo-Sanchez L., Bettini L.R., Sumoy L., Terranova L., Moreira L., Santoro L., Scudeller L., Mesonero F., Roade L., Rühlemann M.C., Schaefer M., Carrabba M., Riveiro-Barciela M., Figuera Basso M.E., Valsecchi M.G., Hernandez-Tejero M., Acosta-Herrera M., D’Angiò M., Baldini M., Cazzaniga M., Schulzky M., Cecconi M., Wittig M., Ciccarelli M., Rodríguez-Gandía M., Bocciolone M., Miozzo M., Montano N., Braun N., Sacchi N., Martínez N., Özer O., Palmieri O., Faverio P., Preatoni P., Bonfanti P., Omodei P., Tentorio P., Castro P., Rodrigues P.M., Blandino Ortiz A., de Cid R., Ferrer R., Gualtierotti R., Nieto R., Goerg S., Badalamenti S., Marsal S., Matullo G., Pelusi S., Juzenas S., Aliberti S., Monzani V., Moreno V., Wesse T., Lenz T.L., Pumarola T., Rimoldi V., Bosari S., Albrecht W., Peter W., Romero-Gómez M., D’Amato M., Duga S., Banales J.M., Hov J.R., Folseraas T., Valenti L., Franke A, & Karlsen T.H. (2020). Genomewide Association Study of Severe Covid-19 with Respiratory Failure. The New England Journal of Medicine.

Publication 2020

Chemagic 360 Global Screening Array (GSA), version 2.0

Freeze Genetic Genome Haplotypes Patients Precision medicine Snps Spanish

Corresponding Organization :

Other organizations : Biogipuzkoa Health Research Institute

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Variable analysis

independent variables

DNA extraction using a Chemagic 360 (PerkinElmer) with the use of the low-volume kit CMG-1491 and the buffy-coat kit CMG-714 (Chemagen)
Genotyping using the Global Screening Array (GSA), version 2.0 (Illumina)
SNP imputation on genome build GRCh38 using the Michigan Imputation Server and 194,512 haplotypes generated by the Trans-Omics for Precision Medicine (TOPMed) program (freeze 5)

dependent variables

Outcome of genotyping and SNP imputation

control variables

Samples excluded during quality control (population outliers)

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