EGAGenomicsWhole Genome Sequencinghttps://ega-archive.org/studies/EGAS00001007573EGAEGA study EGAS00001007573Low-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patientsEGArestrictedCOVID19, Disease, Coronavirus Disease 19, β-CoV, cou, beta-CoV, COVID-19, Genome Sequencing, SARS-CoV-2, Virus Infection, COVID-19 Virus Diseases, 2019 novel coronavirus, 2019 Novel Coronavirus Disease, SARS-CoV-2 Infections, 2019 nCoV Infection, Tl3, COVID 19 Virus Infection, Tl2, Virus Disease, 2019 nCoV Disease, COVID-19 Virus Disease, 2019-nCoV Infection, Lr, Complete Genome, Client., 2019-nCoV Disease, SARS CoV 2 Infection, Infection, Severe Acute Respiratory Syndrome Coronavirus 2 Infection, Coronavirus, Low, COVID-19 Virus Infections, β-coronavirus, 2019-nCoV, COVID 19 Pandemic, me75, Complete, β-CoVs, Whole Genome, betacoronavirus, Disease 2019, Pandemic, COVID-19 Virus Infection, Complete Genome Sequencing, Coronavirus Disease 2019, severe acute respiratory syndrome coronavirus 2, Coronavirus Disease-19, COVID-19 Pandemics, SARS-CoV-2 Infection, COVID-19 Pandemic, beta-CoVs, D17Mit170, T1, Sequencing, SARS-coronavirus 2, COVID-19 Virus, Patient, Clients, Whole, Bra, 2019 Novel Coronavirus Infection, 2019-nCoV Diseases, COVID 19 Virus Disease, SARS Coronavirus 2 Infection, Severe, COVID 19, 2019-nCoV InfectionsIPP2A2, determination, VCFS, Virus Infection, 2019 novel coronavirus, CSMF, Virus Disease, 2019 nCoV Disease, 5730420M11Rik, Techniques, diseases, Method, 2019-nCoV Disease, Associations, DGCR, Equilibrium, DORV, TGA, symptoms, DGS, diseases and disorders, COVID 19 Pandemic, average, SET, human disease, me75, Sex, Genomes, TAF-I, Chromosome Marker, Coronavirus Disease 2019, Coronavirus Disease-19, procedures, beta-CoVs, D17Mit170, T1, Phenotypic, genetic, DmelCG4299, IGAAD, set, NOR-1, Surgical Intensive, Markers, sex, Methodological Studies, DmelCG10574, Allele, Homo sapiens disease, associated, Nucleotide, Frequency, COVID 19 Virus Disease, Genetic Equilibrium, Intensive Care, 2019-nCoV Infections, phapii, screening, β-CoV, wide/broad, CHN, Data Set, familial, 2019-nCoV Infections., SARS-CoV-2, Genome Sequencing, StF-IT-1, 2019 Novel Coronavirus Disease, Normalcy, 2019 nCoV Infection, Procedure, COVID 19 Virus Infection, Tl3, Tl2, Complete Genome, Marker, Frequencies, RENBP, Diseases, Coronavirus, COVID-19 Virus Infections, Individual, nucleotides, Genotypic, Gene Frequencies, HLA-DR-associated protein II, Pandemic, DI-2, Genetic Marker, I-2Dm, signs, DNA Markers, common, Methodological, whole genome, CG4299, Methodological Study, AGE, I-2PP1, Phenotypes, disease, Surgical, wide, Health, TAF-IBETA, Chromosome, Patient, 2019 Novel Coronavirus Infection, inherited genetic, TAF-Ibeta, 2019-nCoV Diseases, DNA, Chromosome Markers, i2pp2a, Allele Frequencies, COVID19, other disease, Intensive, Procedures, Surgical Intensive Care, COVID-19, Gene, COVID-19 Virus Diseases, broad, Normalcies, PHAPII, method, Allele Frequency, CTHM, method used in an experiment, Care, SARS CoV 2 Infection, Studies, Severe Acute Respiratory Syndrome Coronavirus 2 Infection, disease or disorder, Low, β-coronavirus, VCF, 2019-nCoV, Technique, Normalities, study, β-CoVs, Complete, Whole Genome, Genetic, Genotypic Sex, AI573420, COVID-19 Virus Infection, ipp2a2, Complete Genome Sequencing, 2pp2a, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2 Infection, Sequencing, CG10574, non-neoplastic, Study, COVID-19 Virus, 2PP2A, taf-ibeta, Clients, Whole, dSET, dSet, disorder, constitutitional genetic, SARS Coronavirus 2 Infection, Individual Health, Disease, NOR1, Nor1, Coronavirus Disease 19, findings, cou, beta-CoV, Critical, RnBP, disorders, igaad, GlcNAc 2-epimerase, medical condition, SARS-CoV-2 Infections, Client, group, COVID-19 Virus Disease, 2019-nCoV Infection, N-acetyl-D-glucosamine 2-epimerase, Lr, I-2PP2A, chemical analysis, Dm I-2, I2PP2A, Infection, condition, CAFS, background, techniques, betacoronavirus, Disease 2019, MINOR, ensemble, Normality, patient, COVID-19 Pandemics, COVID-19 Pandemic, introduction, SARS-coronavirus 2, plan specification, DNA Marker, TBX1C, dSET/TAF-Ibeta, 2610030F17Rik, Phenotypic Sex, Bra, CATCH22, renin-binding protein, TEC, assay, AA407739, hereditary, Minor, Severe, COVID 19, methodologyfalseLow-coverage whole genome sequencing for a highly selective cohort of severe COVID-19 patientsBackground Despite advances in identification of genetic markers associated to severe COVID-19, the full genetic characterisation of the disease remains elusive. Imputation of low-coverage whole genome sequencing (lcWGS) has emerged as a competitive method to study such disease-related genetic markers as they enable genotyping of most common genetic variants used for genome wide association studies. This study aims at exploring the potential use of imputation in lcWGS for a highly selected severe COVID-19 patient cohort. Findings We generated an imputed dataset of 79 variant call format (VCF) patient files using the GLIMPSE1 tool, each containing, on average, 9.5 million single nucleotide variants. The validation assessment of imputation accuracy yielded a squared Pearson correlation of approximately 0.97 across sequencing platforms, showing that GLIMPSE1 can be used to confidently impute variants with minor allele frequency up to approximately 2% in Spanish ancestry individuals. We conducted a comprehensive analysis on the patient cohort, examining hospitalisation and intensive care utilisation, sex and age-based differences, and clinical phenotypes using a standardised set of medical terms specifically developed to characterise severe COVID-19 symptoms for this cohort. Conclusion This dataset highlights the utility and accuracy of lcWGS imputation in the study of COVID-19 severity, setting a precedent for other applications in resource-constrained environments. The methods and findings presented here may be leveraged in future genomic projects, providing vital insights for health challenges like COVID-19.2023-10-18 15:24:38EGAS000010075739606EGAD00001011363EGAC00001003435