Whole-Exome Sequencing to Identify Rare Genetic Variants
Genomic DNA was extracted from whole blood from all patients except P17, for whom DNA was obtained from SV40-transformed fibroblasts. The whole exome was sequenced at the Genomics Core Facility of the Imagine Institute (Paris, France), the Yale Center for Genome Analysis the New York Genome Center, and The American Genome Center (Uniformed Services University of the Health Sciences, Bethesda, MD, USA), and the Genomics Division–Institute of Technology and Renewable Energies of the Canarian Health System sequencing hub (Canary Islands, Spain), as previously reported (Asano et al., 2021 (link)). The whole-exome sequences of the patients were filtered against the complete International Union of Immunological Societies list of genes (Tangye et al., 2022 (link)), with the retention of variants with an allele frequency below 0.001. We excluded synonymous mutations, downstream, upstream, intron and non-coding transcript variants and intergenic variants. We also excluded variants predicted to be benign and we checked the quality of the exome sequences. The mutation significance cutoff (http://pec630.rockefeller.edu:8080/MSC/) was used to determine whether variants were likely to be damaging.
García-García A., Pérez de Diego R., Flores C., Rinchai D., Solé-Violán J., Deyà-Martínez À., García-Solis B., Lorenzo-Salazar J.M., Hernández-Brito E., Lanz A.L., Moens L., Bucciol G., Almuqamam M., Domachowske J.B., Colino E., Santos-Perez J.L., Marco F.M., Pignata C., Bousfiha A., Turvey S.E., Bauer S., Haerynck F., Ocejo-Vinyals J.G., Lendinez F., Prader S., Naumann-Bartsch N., Pachlopnik Schmid J., Biggs C.M., Hildebrand K., Dreesman A., Cárdenes M.Á., Ailal F., Benhsaien I., Giardino G., Molina-Fuentes A., Fortuny C., Madhavarapu S., Conway D.H., Prando C., Schidlowski L., Martínez de Saavedra Álvarez M.T., Alfaro R., Rodríguez de Castro F., Meyts I., Hauck F., Puel A., Bastard P., Boisson B., Jouanguy E., Abel L., Cobat A., Zhang Q., Casanova J.L., Alsina L, & Rodríguez-Gallego C. (2023). Humans with inherited MyD88 and IRAK-4 deficiencies are predisposed to hypoxemic COVID-19 pneumonia. The Journal of Experimental Medicine, 220(5), e20220170.
Other organizations :
Hospital Sant Joan de Déu Barcelona, Hospital La Paz Institute for Health Research, Instituto Tecnológico y de Energías Renovables, Universidad Fernando Pessoa Canarias, Instituto de Salud Carlos III, Rockefeller University, Hospital Universitario de Gran Canaria Doctor Negrín, Ludwig-Maximilians-Universität München, KU Leuven, Universitair Ziekenhuis Leuven, St. Christopher's Hospital for Children, Drexel University, SUNY Upstate Medical University, Hospital Universitario Insular de Gran Canaria, Hospital Universitario Virgen de las Nieves, Hospital General Universitario de Alicante Doctor Balmis, Federico II University Hospital, University of Hassan II Casablanca, British Columbia Children's Hospital, University of British Columbia, Ghent University Hospital, Ghent University, Marqués de Valdecilla University Hospital, Instituto de Investigación Marqués de Valdecilla, Hospital Materno-Infantil, University Children's Hospital Zurich, University of Zurich, Centre Hospitalier Universitaire de Saint-Pierre, Departament de Salut, Universitat de Barcelona, Universidad de Las Palmas de Gran Canaria, Université Paris Cité, Institut des Maladies Génétiques Imagine, Howard Hughes Medical Institute, Inserm, Assistance Publique – Hôpitaux de Paris
Source of DNA: Whole blood (except for patient P17, for whom DNA was obtained from SV40-transformed fibroblasts)
dependent variables
Whole exome sequencing of patients
control variables
Filtering of whole-exome sequences against the complete International Union of Immunological Societies list of genes
Exclusion of synonymous mutations, downstream, upstream, intron and non-coding transcript variants, and intergenic variants
Exclusion of variants predicted to be benign
Checking the quality of the exome sequences
Using the mutation significance cutoff to determine whether variants were likely to be damaging
controls
No positive or negative controls were explicitly mentioned in the provided information.
Annotations
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