Integrative genomics analysis reveals a 21q22.11 locus contributing risk to COVID-19

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1. Version published to 10.1093/hmg/ddab125

   May 5, 2021
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   Mar 1, 2021

   SciScore for 10.1101/2020.09.16.20195685: (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
   After removing low-quality and non-matched SNPs, there were 8,424,883 high-quality SNPs with a MAF ≥ 1% and ≥ imputation R2 0.6 that were common to both datasets with the use of effect-size estimates (BETA) and their standard errors (SE) for the meta-analysis.	BETA suggested: (BETA, RRID:SCR_007556)
   As reported in Ellinghaus et al. [8], we used the combined P value and combined effect (E) with its SE generated by the METAL to compute the odds ratio (OR) and its 95% confidence interval (CI): 1) OR = exp (E); 2) the upper confidence limit (OR_95 U) = exp (E + 1.96*SE); 3) the lower …

   SciScore for 10.1101/2020.09.16.20195685: (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
   After removing low-quality and non-matched SNPs, there were 8,424,883 high-quality SNPs with a MAF ≥ 1% and ≥ imputation R2 0.6 that were common to both datasets with the use of effect-size estimates (BETA) and their standard errors (SE) for the meta-analysis.	BETA suggested: (BETA, RRID:SCR_007556)
   As reported in Ellinghaus et al. [8], we used the combined P value and combined effect (E) with its SE generated by the METAL to compute the odds ratio (OR) and its 95% confidence interval (CI): 1) OR = exp (E); 2) the upper confidence limit (OR_95 U) = exp (E + 1.96*SE); 3) the lower confidence limit (OR_95L) = exp (E - 1.96*SE).	METAL suggested: (METAL, RRID:SCR_002013)
   The web-access tool of LocusZoom [31] was used to visualize regional association plots (http://locuszoom.sph.umich.edu/).	LocusZoom suggested: (LOCUSZOOM, RRID:SCR_009257)
   Using the overrepresentation analysis, the WebGestalt could identify functional association between COVID-19-associated genes and KEGG pathways.	WebGestalt suggested: None KEGG suggested: (KEGG, RRID:SCR_012773)
   These estimated weights are processed with beta values and standard errors from meta-GWAS summary data on COVID-19 to predict gene expression from GWAS summary statistics, while combining the variance and co-variance of SNPs from an LD reference panel based on the 1000 Genomes Project Phase 3 genotypes [33].	1000 Genomes Project suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
   Drug-gene interaction analysis: We submitted these 11 COVID-19-associated genes into the widely-used Drug Gene Interaction Database (DGIdb v.3.0.2; http://www.dgidb.org/) to identify drug-gene interactions with Food and Drug Administration (FDA)-approved pharmaceutical compounds as well as antineoplastic and immunotherapies drugs depended on 20 databases with 51 known interaction types, and search 10 databases to find genes with potential drug abilities.	DGIdb suggested: (DGIdb, RRID:SCR_006608)

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   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.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04331899	Active, not recruiting	Single-Blind Study of a Single Dose of Peginterferon Lambda-…

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.09.16.20195685v1 on medRxiv

   Sep 18, 2020