A genome-wide association study of COVID-19 related hospitalization in Spain reveals genetic disparities among sexes
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
We describe the results of the Spanish Coalition to Unlock Research on Host Genetics on COVID-19 (SCOURGE). In sex-disaggregated genome-wide studies of COVID-19 hospitalization, we found two known loci associated among males ( SLC6A20 - LZTFL1 and IFNAR2 ), and a novel one among females ( TLE1 ). Meta-analyses with independent studies revealed two novel associations ( AQP3 and ARHGAP33 ) and replicated ELF5 . A genetic risk score predicted COVID-19 severity, especially among younger males. We found less SNP-heritability and larger heritability differences by age (<60/≥60 years) among males than females. Inbreeding depression was associated with COVID-19 hospitalization and severity, and the effect was stronger among older males.
Article activity feed
-
SciScore for 10.1101/2021.11.24.21266741: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Study data were collected and managed using REDCap electronic data capture tools hosted at Centro de Investigación Biomédica en Red (CIBER) [57, 58] (Supplementary Note). REDCapsuggested: (REDCap, RRID:SCR_003445)First, a list of probe sets was removed based on poor cluster separation or excessive minor allele frequency (MAF) difference from The 1000 Genomes Project data (1KGP) [59]. 1000 Genomes Projectsuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)Ancestry was then inferred with Admixture [63] using the defined 1KGP superpopulations. Admixturesuggested: (ADMIXTURE, RRID:SCR_001…SciScore for 10.1101/2021.11.24.21266741: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Study data were collected and managed using REDCap electronic data capture tools hosted at Centro de Investigación Biomédica en Red (CIBER) [57, 58] (Supplementary Note). REDCapsuggested: (REDCap, RRID:SCR_003445)First, a list of probe sets was removed based on poor cluster separation or excessive minor allele frequency (MAF) difference from The 1000 Genomes Project data (1KGP) [59]. 1000 Genomes Projectsuggested: (1000 Genomes Project and AWS, RRID:SCR_008801)Ancestry was then inferred with Admixture [63] using the defined 1KGP superpopulations. Admixturesuggested: (ADMIXTURE, RRID:SCR_001263)Then, the main results of both Spanish cohorts (SCOURGE and CNIO) for the overall and sex-stratified analyses were meta-analysed assuming a fixed-effects model using METAL [68]. METALsuggested: (METAL, RRID:SCR_002013)VEP (https://www.ensembl.org/info/docs/tools/vep/index.html) and the V2G aggregate scoring from Open Targets Genetics (https://genetics.opentargets.org) were used to annotate the most prominent biological effects of the variants in the credible sets. https://www.ensembl.org/info/docs/tools/vep/index.htmlsuggested: NoneROH calling: The ROH segments longer than 300 Kb were called in SCOURGE using PLINK 1.9 in the European QC-ed genotyped dataset (before imputation) with the following parameters: homozyg-snp 30, homozyg-kb 300, homozyg-density 30, homozyg-window-sn 30, homozyg-gap 1000, homozyg-window-het 1, homozyg-window-missing 5, homozyg-window-threshold 0.05. PLINKsuggested: (PLINK, RRID:SCR_001757)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04374279 Withdrawn Trial to Promote Recovery From COVID-19 With Endocrine Thera… NCT04397718 Completed Hormonal Intervention for the Treatment in Veterans With COV… NCT04345887 Completed Spironolactone in Covid-19 Induced ARDS Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-
