Whole-exome sequencing with at least 97% coverage at 20x was performed using the Illumina NovaSeq6000 System (Illumina, San Diego, CA, USA). Library preparation was performed using the Illumina Exome Panel (Illumina) according to the manufacturer's protocol. Library enrichment was tested by qPCR, and the size distribution and concentration were determined using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The NovaSeq6000 System (Illumina) was used for DNA sequencing through 150 bp paired-end reads. Variant calling was performed according to the GATK4 (O’Connor and Auwera 2020 ) best practice guidelines, using BWA (Li and Durbin 2010 (link)) for mapping and ANNOVAR (Wang et al. 2010 (link)) for annotating.
Fallerini C., Picchiotti N., Baldassarri M., Zguro K., Daga S., Fava F., Benetti E., Amitrano S., Bruttini M., Palmieri M., Croci S., Lista M., Beligni G., Valentino F., Meloni I., Tanfoni M., Minnai F., Colombo F., Cabri E., Fratelli M., Gabbi C., Mantovani S., Frullanti E., Gori M., Crawley F.P., Butler-Laporte G., Richards B., Zeberg H., Lipcsey M., Hultström M., Ludwig K.U., Schulte E.C., Pairo-Castineira E., Baillie J.K., Schmidt A., Frithiof R., Mari F., Renieri A, & Furini S. (2021). Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity. Human Genetics, 141(1), 147-173.
Other organizations :
University of Pavia, Institute of Biomedical Technologies, Mario Negri Institute for Pharmacological Research, Karolinska Institutet, Policlinico San Matteo Fondazione, Istituti di Ricovero e Cura a Carattere Scientifico, Centre National de la Recherche Scientifique, European Forum for Good Clinical Practice, Jewish General Hospital, McGill University, King's College London, Uppsala University, University Hospital Bonn, University of Bonn, Ludwig-Maximilians-Universität München, Helmholtz Zentrum München, Roslin Institute, University of Edinburgh, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh Royal Infirmary
Size distribution and concentration determined using Agilent Bioanalyzer 2100
150 bp paired-end reads
controls
No positive or negative controls were explicitly mentioned.
Annotations
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